---
_id: '12723'
abstract:
- lang: eng
text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties.
To explain their origin, it is necessary to study how electromagnetic fields interact
with these systems. We address this problem here by studying two classical quantities:
Faraday rotation and the complex refractive index in a paradigmatic perovskite
CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of
electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the
observed data even on the qualitative level. To amend this, we demonstrate that
there exists a relevant atomic-level coupling between electromagnetic fields and
the spin degree of freedom. This spin-electric coupling allows for quantitative
description of a number of previous as well as present experimental data. In particular,
we use it here to show that the Faraday effect in lead halide perovskites is dominated
by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel
contribution. Finally, we present general symmetry-based phenomenological arguments
that in the low-energy limit our effective model includes all basis coupling terms
to the electromagnetic field in the linear order.'
article_number: '106901'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan A.
full_name: Zhumekenov, Ayan A.
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead
halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide
perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev.
“Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.
ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,”
Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites.
Physical Review Letters. 130(10), 106901.
mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.”
Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society,
2023, doi:10.1103/physrevlett.130.106901.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).
date_created: 2023-03-14T13:11:59Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T13:39:04Z
day: '10'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevlett.130.106901
external_id:
arxiv:
- '2203.09443'
isi:
- '000982435900002'
intvolume: ' 130'
isi: 1
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.09443
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-electric coupling in lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12724'
abstract:
- lang: eng
text: 'We use general symmetry-based arguments to construct an effective model suitable
for studying optical properties of lead halide perovskites. To build the model,
we identify an atomic-level interaction between electromagnetic fields and the
spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian.
As a first application, we study two basic optical characteristics of the material:
the Verdet constant and the refractive index. Beyond these linear characteristics
of the material, the model is suitable for calculating nonlinear effects such
as the third-order optical susceptibility. Analysis of this quantity shows that
the geometrical properties of the spin-electric term imply isotropic optical response
of the system, and that optical anisotropy of lead halide perovskites is a manifestation
of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.'
article_number: '125201'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan
full_name: Zhumekenov, Ayan
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical
properties of lead halide perovskites. Physical Review B. 2023;107(12).
doi:10.1103/physrevb.107.125201
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical
properties of lead halide perovskites. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.107.125201
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective
Model for Studying Optical Properties of Lead Halide Perovskites.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.
ieee: A. Volosniev et al., “Effective model for studying optical properties
of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American
Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties
of lead halide perovskites. Physical Review B. 107(12), 125201.
mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of
Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201,
American Physical Society, 2023, doi:10.1103/physrevb.107.125201.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).
date_created: 2023-03-14T13:13:05Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:39:47Z
day: '15'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevb.107.125201
external_id:
arxiv:
- '2204.04022'
isi:
- '000972602200006'
intvolume: ' 107'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.04022
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective model for studying optical properties of lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12759'
abstract:
- lang: eng
text: Stereological methods for estimating the 3D particle size and density from
2D projections are essential to many research fields. These methods are, however,
prone to errors arising from undetected particle profiles due to sectioning and
limited resolution, known as ‘lost caps’. A potential solution developed by Keiding,
Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for
lost caps by quantifying the smallest detectable profile in terms of its limiting
‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the
section surface. However, this simple solution has not been widely adopted nor
tested. Rather, model-independent design-based stereological methods, which do
not explicitly account for lost caps, have come to the fore. Here, we provide
the first experimental validation of the Keiding model by comparing the size and
density of particles estimated from 2D projections with direct measurement from
3D EM reconstructions of the same tissue. We applied the Keiding model to estimate
the size and density of somata, nuclei and vesicles in the cerebellum of mice
and rats, where high packing density can be problematic for design-based methods.
Our analysis reveals a Gaussian distribution for ϕ rather than a single value.
Nevertheless, curve fits of the Keiding model to the 2D diameter distribution
accurately estimate the mean ϕ and 3D diameter distribution. While systematic
testing using simulations revealed an upper limit to determining ϕ, our analysis
shows that estimated ϕ can be used to determine the 3D particle density from the
2D density under a wide range of conditions, and this method is potentially more
accurate than minimum-size-based lost-cap corrections and disector methods. Our
results show the Keiding model provides an efficient means of accurately estimating
the size and density of particles from 2D projections even under conditions of
a high density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical
support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments
and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048;
224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal
Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung
der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z
312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding
from the European Research Council (ERC; https://erc.europa.eu) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692).
NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
full_name: Rothman, Jason Seth
last_name: Rothman
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Noemi
full_name: Holderith, Noemi
last_name: Holderith
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: R.
full_name: Angus Silver, R.
last_name: Angus Silver
citation:
ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation
of a stereological method for estimating particle size and density from 2D projections
with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148
apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus
Silver, R. (2023). Validation of a stereological method for estimating particle
size and density from 2D projections with high accuracy. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0277148
chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M
Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.
ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus
Silver, “Validation of a stereological method for estimating particle size and
density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no.
3 March. Public Library of Science, 2023.
ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023.
Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.
mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE,
vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.
short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:46:39Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
isi:
- '001024737400001'
file:
- access_level: open_access
checksum: 2380331ec27cc87808826fc64419ac1c
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:51:09Z
date_updated: 2023-03-27T06:51:09Z
file_id: '12770'
file_name: 2023_PLoSOne_Rothman.pdf
file_size: 7290413
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:45:54Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2023'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
and function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:45:12Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...
---
_id: '12787'
abstract:
- lang: eng
text: "Populations evolve in spatially heterogeneous environments. While a certain
trait might bring a fitness advantage in some patch of the environment, a different
trait might be advantageous in another patch. Here, we study the Moran birth–death
process with two types of individuals in a population stretched across two patches
of size N, each patch favouring one of the two types. We show that the long-term
fate of such populations crucially depends on the migration rate μ\r\n between
the patches. To classify the possible fates, we use the distinction between polynomial
(short) and exponential (long) timescales. We show that when μ is high then one
of the two types fixates on the whole population after a number of steps that
is only polynomial in N. By contrast, when μ is low then each type holds majority
in the patch where it is favoured for a number of steps that is at least exponential
in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates
those two scenarios, thereby exactly delineating the situations that support long-term
coexistence of the two types. We also discuss the case of various cycle graphs
and we present computer simulations that perfectly match our analytical results."
acknowledgement: J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)
article_number: '20220685'
article_processing_charge: No
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran
process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685'
apa: 'Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence
times in the Moran process with environmental heterogeneity. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rspa.2022.0685'
chicago: 'Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee.
“Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.'
ieee: 'J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in
the Moran process with environmental heterogeneity,” Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no.
2271. The Royal Society, 2023.'
ista: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the
Moran process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.'
mla: 'Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental
Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society,
2023, doi:10.1098/rspa.2022.0685.'
short: 'J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences 479 (2023).'
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2023-08-01T13:58:34Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rspa.2022.0685
ec_funded: 1
external_id:
isi:
- '000957125500002'
file:
- access_level: open_access
checksum: 13953d349fbefcb5d21ccc6b303297eb
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:25:29Z
date_updated: 2023-04-03T06:25:29Z
file_id: '12796'
file_name: 2023_ProceedingsRoyalSocietyA_Svoboda.pdf
file_size: 827784
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:25:29Z
has_accepted_license: '1'
intvolume: ' 479'
isi: 1
issue: '2271'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
eissn:
- 1471-2946
issn:
- 1364-5021
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: research_data
url: https://doi.org/10.6084/m9.figshare.21261771.v1
scopus_import: '1'
status: public
title: Coexistence times in the Moran process with environmental heterogeneity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 479
year: '2023'
...
---
_id: '12788'
abstract:
- lang: eng
text: We show that the simplest of existing molecules—closed-shell diatomics not
interacting with one another—host topological charges when driven by periodic
far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped
onto a “crystalline” lattice in angular momentum space. This allows us to define
quasimomenta and the band structure in the Floquet representation, by analogy
with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3
of the molecular rotational period creates a lattice with three atoms per unit
cell with staggered hopping. Within the synthetic dimension of the laser strength,
we discover Dirac cones with topological charges. These Dirac cones, topologically
protected by reflection and time-reversal symmetry, are reminiscent of (although
not equivalent to) that seen in graphene. They—and the corresponding edge states—are
broadly tunable by adjusting the laser strength and can be observed in present-day
experiments by measuring molecular alignment and populations of rotational levels.
This paves the way to study controllable topological physics in gas-phase experiments
with small molecules as well as to classify dynamical molecular states by their
topological invariants.
acknowledgement: M. L. acknowledges support by the European Research Council (ERC)
Starting Grant No. 801770 (ANGULON).
article_number: '103202'
article_processing_charge: No
article_type: original
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked
molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202
apa: Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of
periodically kicked molecules. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.130.103202
chicago: Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges
of Periodically Kicked Molecules.” Physical Review Letters. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.
ieee: V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically
kicked molecules,” Physical Review Letters, vol. 130, no. 10. American
Physical Society, 2023.
ista: Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically
kicked molecules. Physical Review Letters. 130(10), 103202.
mla: Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.”
Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society,
2023, doi:10.1103/PhysRevLett.130.103202.
short: V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T14:02:06Z
day: '10'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.130.103202
ec_funded: 1
external_id:
arxiv:
- '2206.07067'
isi:
- '000957635500003'
intvolume: ' 130'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2206.07067
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/topology-of-rotating-molecules/
scopus_import: '1'
status: public
title: Topological charges of periodically kicked molecules
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12790'
abstract:
- lang: eng
text: Motivated by the recent discoveries of superconductivity in bilayer and trilayer
graphene, we theoretically investigate superconductivity and other interaction-driven
phases in multilayer graphene stacks. To this end, we study the density of states
of multilayer graphene with up to four layers at the single-particle band structure
level in the presence of a transverse electric field. Among the considered structures,
tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density
of states. We study the phases that can arise in ABCA graphene by tuning the carrier
density and transverse electric field. For a broad region of the tuning parameters,
the presence of strong Coulomb repulsion leads to a spontaneous spin and valley
symmetry breaking via Stoner transitions. Using a model that incorporates the
spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism
for superconductivity driven by repulsive Coulomb interactions. We find that the
strongest superconducting instability is in the p-wave channel, and occurs in
proximity to the onset of Stoner transitions. Interestingly, we find a range of
densities and transverse electric fields where superconductivity develops out
of a strongly corrugated, singly connected Fermi surface in each valley, leading
to a topologically nontrivial chiral p+ip superconducting state with an even number
of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked
tetralayer graphene as a promising platform for observing strongly correlated
physics and topological superconductivity.
acknowledgement: E.B. and T.H. were supported by the European Research Council (ERC)
under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science
Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.
article_number: '104502'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical
Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502
apa: Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes
as a platform for interaction-driven physics and topological superconductivity.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502
chicago: Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer
Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.
ieee: A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as
a platform for interaction-driven physics and topological superconductivity,”
Physical Review B, vol. 107, no. 10. American Physical Society, 2023.
ista: Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical Review
B. 107(10), 104502.
mla: Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven
Physics and Topological Superconductivity.” Physical Review B, vol. 107,
no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.
short: A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:59:29Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1103/PhysRevB.107.104502
external_id:
arxiv:
- '2211.02492'
isi:
- '000945526400003'
intvolume: ' 107'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.02492
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/
scopus_import: '1'
status: public
title: Multilayer graphenes as a platform for interaction-driven physics and topological
superconductivity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12791'
abstract:
- lang: eng
text: We investigate the capabilities of Physics-Informed Neural Networks (PINNs)
to reconstruct turbulent Rayleigh–Bénard flows using only temperature information.
We perform a quantitative analysis of the quality of the reconstructions at various
amounts of low-passed-filtered information and turbulent intensities. We compare
our results with those obtained via nudging, a classical equation-informed data
assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct
with high precision, comparable to the one achieved with nudging. At high Rayleigh
numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction
of the velocity fields only when data for temperature is provided with high spatial
and temporal density. When data becomes sparse, the PINNs performance worsens,
not only in a point-to-point error sense but also, and contrary to nudging, in
a statistical sense, as can be seen in the probability density functions and energy
spectra.
acknowledgement: This project has received partial funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(Grant Agreement No. 882340))
article_number: '16'
article_processing_charge: No
article_type: original
author:
- first_name: Patricio
full_name: Clark Di Leoni, Patricio
last_name: Clark Di Leoni
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Michele
full_name: Buzzicotti, Michele
last_name: Buzzicotti
- first_name: Luca
full_name: Biferale, Luca
last_name: Biferale
citation:
ama: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard
flows out of temperature-only measurements using Physics-Informed Neural Networks.
The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9
apa: Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023).
Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks. The European Physical Journal E. Springer
Nature. https://doi.org/10.1140/epje/s10189-023-00276-9
chicago: Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and
Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements
Using Physics-Informed Neural Networks.” The European Physical Journal E.
Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.
ieee: P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer
Nature, 2023.
ista: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks. The European Physical Journal E. 46(3), 16.
mla: Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out
of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The
European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.
short: P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European
Physical Journal E 46 (2023).
date_created: 2023-04-02T22:01:11Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-01T14:03:47Z
day: '20'
department:
- _id: CaMu
doi: 10.1140/epje/s10189-023-00276-9
external_id:
arxiv:
- '2301.07769'
isi:
- '000956387200001'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2301.07769'
month: '03'
oa: 1
oa_version: Preprint
publication: The European Physical Journal E
publication_identifier:
eissn:
- 1292-895X
issn:
- 1292-8941
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 46
year: '2023'
...
---
_id: '12830'
abstract:
- lang: eng
text: Interstitial fluid (IF) accumulation between embryonic cells is thought to
be important for embryo patterning and morphogenesis. Here, we identify a positive
mechanical feedback loop between cell migration and IF relocalization and find
that it promotes embryonic axis formation during zebrafish gastrulation. We show
that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between
the yolk cell and deep cell tissue to extend the embryonic axis, compress the
overlying deep cell layer, thereby causing IF to flow from the deep cell layer
to the boundary between the yolk cell and the deep cell layer, directly ahead
of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion
formation and migration by opening up the space into which the ppl moves and,
thereby, the ability of the ppl to trigger IF relocalization by pushing against
the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic
feedback loop between cell migration and IF relocalization.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful
discussions and support with the SPIM experiments; the Heisenberg group, and especially
Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović
(ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and
zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia
Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura
(Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work
was supported by funding from the European Union (European Research Council Advanced
grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and
HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des
deutschen Volkes to F.P.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Friedrich
full_name: Preusser, Friedrich
last_name: Preusser
- first_name: Irene
full_name: Steccari, Irene
id: 2705C766-9FE2-11EA-B224-C6773DDC885E
last_name: Steccari
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop
between mesendoderm cell migration and interstitial fluid relocalization promotes
embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7.
doi:10.1016/j.devcel.2023.02.016
apa: Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I.,
Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between
mesendoderm cell migration and interstitial fluid relocalization promotes embryonic
axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016
chicago: Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser,
Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg.
“A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial
Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental
Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.
ieee: K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7,
2023.
ista: Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM,
Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish. Developmental Cell. 58(7), 582–596.e7.
mla: Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration
and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.”
Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.
short: K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M.
Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:10:38Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1016/j.devcel.2023.02.016
ec_funded: 1
external_id:
isi:
- '000982111800001'
file:
- access_level: open_access
checksum: c80ca2ebc241232aacdb5aa4b4c80957
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:41:25Z
date_updated: 2023-04-17T07:41:25Z
file_id: '12842'
file_name: 2023_DevelopmentalCell_Huljev.pdf
file_size: 7925886
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:41:25Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 582-596.e7
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 266BC5CE-B435-11E9-9278-68D0E5697425
grant_number: LT000429
name: Coordination of mesendoderm fate specification and internalization during
zebrafish gastrulation
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A hydraulic feedback loop between mesendoderm cell migration and interstitial
fluid relocalization promotes embryonic axis formation in zebrafish
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2023'
...
---
_id: '12831'
abstract:
- lang: eng
text: The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations
of a many-body bath, can be used to describe an impurity rotating in a fluid or
solid environment. Here, we propose a coherent state ansatz in the co-rotating
frame, which provides a comprehensive theoretical description of angulons. We
reveal the quasiparticle properties, such as energies, quasiparticle weights,
and spectral functions, and show that our ansatz yields a persistent decrease
in the impurity’s rotational constant due to many-body dressing, which is consistent
with experimental observations. From our study, a picture of the angulon emerges
as an effective spin interacting with a magnetic field that is self-consistently
generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy,
which focuses on the response of rotating molecules to a laser perturbation in
the linear response regime. Importantly, we take into account initial-state interactions
that have been neglected in prior studies and reveal their impact on the excitation
spectrum. To examine the angulon instability regime, we use a single-excitation
ansatz and obtain results consistent with experiments, in which a broadening of
spectral lines is observed while phonon wings remain highly suppressed due to
initial-state interactions.
acknowledgement: We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt
for their valuable discussions. We acknowledge support by the Max Planck Society
and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC
2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges
support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
T.S. is supported by the National Key Research and Development Program of China
(Grant No. 2017YFA0718304) and the National Natural Science Foundation of China
(Grant Nos. 11974363, 12135018, and 12047503).
article_number: '134301'
article_processing_charge: No
article_type: original
author:
- first_name: Zhongda
full_name: Zeng, Zhongda
last_name: Zeng
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Tao
full_name: Shi, Tao
last_name: Shi
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
citation:
ama: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons
and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13).
doi:10.1063/5.0135893
apa: Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational
theory of angulons and their rotational spectroscopy. The Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893
chicago: Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard
Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893.
ieee: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory
of angulons and their rotational spectroscopy,” The Journal of Chemical Physics,
vol. 158, no. 13. American Institute of Physics, 2023.
ista: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory
of angulons and their rotational spectroscopy. The Journal of Chemical Physics.
158(13), 134301.
mla: Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational
Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301,
American Institute of Physics, 2023, doi:10.1063/5.0135893.
short: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical
Physics 158 (2023).
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-07T00:00:00Z
date_updated: 2023-08-01T14:08:47Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0135893
ec_funded: 1
external_id:
arxiv:
- '2211.08070'
isi:
- '000970038800001'
file:
- access_level: open_access
checksum: 8d801babea4df48e08895c76571bb19e
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:28:38Z
date_updated: 2023-04-17T07:28:38Z
file_id: '12841'
file_name: 2023_JourChemicalPhysics_Zeng.pdf
file_size: 7388057
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:28:38Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '13'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variational theory of angulons and their rotational spectroscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2023'
...
---
_id: '12839'
abstract:
- lang: eng
text: Universal nonequilibrium properties of isolated quantum systems are typically
probed by studying transport of conserved quantities, such as charge or spin,
while transport of energy has received considerably less attention. Here, we study
infinite-temperature energy transport in the kinetically constrained PXP model
describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations,
including exact diagonalization and time-evolving block decimation methods, reveal
the existence of two distinct transport regimes. At moderate times, the energy-energy
correlation function displays periodic oscillations due to families of eigenstates
forming different su(2) representations hidden within the spectrum. These families
of eigenstates generalize the quantum many-body scarred states found in previous
works and leave an imprint on the infinite-temperature energy transport. At later
times, we observe a long-lived superdiffusive transport regime that we attribute
to the proximity of a nearby integrable point. While generic strong deformations
of the PXP model indeed restore diffusive transport, adding a strong chemical
potential intriguingly gives rise to a well-converged superdiffusive exponent
z≈3/2. Our results suggest constrained models to be potential hosts of novel transport
regimes and call for developing an analytic understanding of their energy transport.
acknowledgement: "We would like to thank Alexios Michailidis, Sarang Gopalakrishnan,
and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support
by the European Research Council under the European Union’s Horizon 2020 research
and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge
support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership
Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research
data: This publication is theoretical work that does not require supporting research
data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International
Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for
awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations
were performed. The TEBD\r\nsimulations were performed using the ITENSOR library
[54]."
article_number: '011033'
article_processing_charge: No
article_type: original
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Jean Yves
full_name: Desaules, Jean Yves
last_name: Desaules
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033
apa: Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive
energy transport in kinetically constrained models. Physical Review X.
American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033
chicago: Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić.
“Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical
Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.
ieee: M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy
transport in kinetically constrained models,” Physical Review X, vol. 13,
no. 1. American Physical Society, 2023.
ista: Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 13(1), 011033.
mla: Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained
Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society,
2023, doi:10.1103/PhysRevX.13.011033.
short: M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).
date_created: 2023-04-16T22:01:09Z
date_published: 2023-03-07T00:00:00Z
date_updated: 2023-08-01T14:11:28Z
day: '07'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevX.13.011033
ec_funded: 1
external_id:
isi:
- '000957625700001'
file:
- access_level: open_access
checksum: ee060cea609af79bba7af74b1ce28078
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T08:36:53Z
date_updated: 2023-04-17T08:36:53Z
file_id: '12845'
file_name: 2023_PhysReviewX_Ljubotina.pdf
file_size: 1958523
relation: main_file
success: 1
file_date_updated: 2023-04-17T08:36:53Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superdiffusive energy transport in kinetically constrained models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '12822'
abstract:
- lang: eng
text: Gears and cogwheels are elemental components of machines. They restrain degrees
of freedom and channel power into a specified motion. Building and powering small-scale
cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy
injection, and control are, however, a challenge at the microscale. In contrast
with passive gears, whose function is to transmit torques from one to another,
interlocking and untethered active gears have the potential to unveil dynamics
and functions untapped by externally driven mechanisms. Here, it is shown the
assembly and control of a family of self-spinning cogwheels with varying teeth
numbers and study the interlocking of multiple cogwheels. The teeth are formed
by colloidal microswimmers that power the structure. The cogwheels are autonomous
and active, showing persistent rotation. Leveraging the angular momentum of optical
vortices, we control the direction of rotation of the cogwheels. The pairs of
interlocking and active cogwheels that roll over each other in a random walk and
have curvature-dependent mobility are studied. This behavior is leveraged to self-position
parts and program microbots, demonstrating the ability to pick up, direct, and
release a load. The work constitutes a step toward autonomous machinery with external
control as well as (re)programmable microbots and matter.
acknowledgement: 'Army Research Office. Grant Number: W911NF-20-1-0112'
article_number: '2200129'
article_processing_charge: No
article_type: original
author:
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning
of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129
apa: Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking,
and self‐positioning of active cogwheels. Advanced Intelligent Systems.
Wiley. https://doi.org/10.1002/aisy.202200129
chicago: Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control,
Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent
Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129.
ieee: Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking,
and self‐positioning of active cogwheels,” Advanced Intelligent Systems,
vol. 5, no. 1. Wiley, 2023.
ista: Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and
self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.
mla: Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning
of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129,
Wiley, 2023, doi:10.1002/aisy.202200129.
short: Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).
date_created: 2023-04-12T08:30:03Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T14:06:50Z
day: '01'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1002/aisy.202200129
external_id:
arxiv:
- '2201.03333'
isi:
- '000852291200001'
file:
- access_level: open_access
checksum: d48fc41d39892e7fa0d44cb352dd46aa
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T06:44:17Z
date_updated: 2023-04-17T06:44:17Z
file_id: '12840'
file_name: 2023_AdvancedIntelligentSystems_Martinet.pdf
file_size: 2414125
relation: main_file
success: 1
file_date_updated: 2023-04-17T06:44:17Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Advanced Intelligent Systems
publication_identifier:
issn:
- 2640-4567
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Rotation control, interlocking, and self‐positioning of active cogwheels
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '12818'
abstract:
- lang: eng
text: The multicellular organization of diverse systems, including embryos, intestines,
and tumors relies on coordinated cell migration in curved environments. In these
settings, cells establish supracellular patterns of motion, including collective
rotation and invasion. While such collective modes have been studied extensively
in flat systems, the consequences of geometrical and topological constraints on
collective migration in curved systems are largely unknown. Here, we discover
a collective mode of cell migration in rotating spherical tissues manifesting
as a propagating single-wavelength velocity wave. This wave is accompanied by
an apparently incompressible supracellular flow pattern featuring topological
defects as dictated by the spherical topology. Using a minimal active particle
model, we reveal that this collective mode arises from the effect of curvature
on the active flocking behavior of a cell layer confined to a spherical surface.
Our results thus identify curvature-induced velocity waves as a mode of collective
cell migration, impacting the dynamical organization of 3D curved tissues.
acknowledgement: We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti,
and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B.
is a NOMIS fellow supported by the NOMIS foundation and was in part supported by
a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM)
and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science
Program (LT000475/2018-C) and from the National Science Foundation, through the
Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support
from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open
Access funding enabled and organized by Projekt DEAL.
article_number: '1643'
article_processing_charge: No
article_type: original
author:
- first_name: Tom
full_name: Brandstätter, Tom
last_name: Brandstätter
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Yu Long
full_name: Han, Yu Long
last_name: Han
- first_name: Ricard
full_name: Alert, Ricard
last_name: Alert
- first_name: Ming
full_name: Guo, Ming
last_name: Guo
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
2023;14. doi:10.1038/s41467-023-37054-2
apa: Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz,
C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2
chicago: Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo,
and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical
Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.
ieee: T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz,
“Curvature induces active velocity waves in rotating spherical tissues,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
14, 1643.
mla: Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating
Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature,
2023, doi:10.1038/s41467-023-37054-2.
short: T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz,
Nature Communications 14 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-24T00:00:00Z
date_updated: 2023-08-01T14:05:30Z
day: '24'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-023-37054-2
external_id:
isi:
- '000959887700008'
pmid:
- '36964141'
file:
- access_level: open_access
checksum: 54f06f9eee11d43bab253f3492c983ba
content_type: application/pdf
creator: dernst
date_created: 2023-04-11T06:27:00Z
date_updated: 2023-04-11T06:27:00Z
file_id: '12821'
file_name: 2023_NatureComm_Brandstaetter.pdf
file_size: 4146777
relation: main_file
success: 1
file_date_updated: 2023-04-11T06:27:00Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature induces active velocity waves in rotating spherical tissues
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12819'
abstract:
- lang: eng
text: 'Reaching a high cavity population with a coherent pump in the strong-coupling
regime of a single-atom laser is impossible due to the photon blockade effect.
In this Letter, we experimentally demonstrate that in a single-atom maser based
on a transmon strongly coupled to two resonators, it is possible to pump over
a dozen photons into the system. The first high-quality resonator plays the role
of a usual lasing cavity, and the second one presents a controlled dissipation
channel, bolstering population inversion, and modifies the energy-level structure
to lift the blockade. As confirmation of the lasing action, we observe conventional
laser features such as a narrowing of the emission linewidth and external signal
amplification. Additionally, we report unique single-atom features: self-quenching
and several lasing thresholds.'
acknowledgement: We thank N.N. Abramov for assistance with the experimental setup.
The sample was fabricated using equipment of MIPT Shared Facilities Center. This
research was supported by Russian Science Foundation, grant no. 21-72-30026.
article_number: L031701
article_processing_charge: No
article_type: letter_note
author:
- first_name: Alesya
full_name: Sokolova, Alesya
id: 2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a
last_name: Sokolova
orcid: 0000-0002-8308-4144
- first_name: D. A.
full_name: Kalacheva, D. A.
last_name: Kalacheva
- first_name: G. P.
full_name: Fedorov, G. P.
last_name: Fedorov
- first_name: O. V.
full_name: Astafiev, O. V.
last_name: Astafiev
citation:
ama: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade
in a circuit-QED single-atom maser with engineered metastability and strong coupling.
Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701
apa: Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023).
Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.107.L031701
chicago: Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming
Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability
and Strong Coupling.” Physical Review A. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevA.107.L031701.
ieee: A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming
photon blockade in a circuit-QED single-atom maser with engineered metastability
and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical
Society, 2023.
ista: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon
blockade in a circuit-QED single-atom maser with engineered metastability and
strong coupling. Physical Review A. 107(3), L031701.
mla: Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom
Maser with Engineered Metastability and Strong Coupling.” Physical Review A,
vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.
short: A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review
A 107 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-22T00:00:00Z
date_updated: 2023-08-01T14:06:05Z
day: '22'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.107.L031701
external_id:
arxiv:
- '2209.05165'
isi:
- '000957799000006'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2209.05165
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12861'
abstract:
- lang: eng
text: The field of indirect reciprocity investigates how social norms can foster
cooperation when individuals continuously monitor and assess each other’s social
interactions. By adhering to certain social norms, cooperating individuals can
improve their reputation and, in turn, receive benefits from others. Eight social
norms, known as the “leading eight," have been shown to effectively promote the
evolution of cooperation as long as information is public and reliable. These
norms categorize group members as either ’good’ or ’bad’. In this study, we examine
a scenario where individuals instead assign nuanced reputation scores to each
other, and only cooperate with those whose reputation exceeds a certain threshold.
We find both analytically and through simulations that such quantitative assessments
are error-correcting, thus facilitating cooperation in situations where information
is private and unreliable. Moreover, our results identify four specific norms
that are robust to such conditions, and may be relevant for helping to sustain
cooperation in natural populations.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support
by the Stochastic Analysis and Application Research Center (SAARC) under National
Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally
thank Stefan Schmid for providing access to his lab infrastructure at the University
of Vienna for the purpose of collecting simulation data.'
article_number: '2086'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Farbod
full_name: Ekbatani, Farbod
last_name: Ekbatani
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize
indirect reciprocity under imperfect information. Nature Communications.
2023;14. doi:10.1038/s41467-023-37817-x
apa: Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative
assessment can stabilize indirect reciprocity under imperfect information. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x
chicago: Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee.
“Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.
ieee: L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment
can stabilize indirect reciprocity under imperfect information,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment
can stabilize indirect reciprocity under imperfect information. Nature Communications.
14, 2086.
mla: Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity
under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer
Nature, 2023, doi:10.1038/s41467-023-37817-x.
short: L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14
(2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2023-08-01T14:15:57Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-37817-x
ec_funded: 1
external_id:
isi:
- '001003644100020'
pmid:
- '37045828'
file:
- access_level: open_access
checksum: a4b3b7b36fbef068cabf4fb99501fef6
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T09:13:53Z
date_updated: 2023-04-25T09:13:53Z
file_id: '12868'
file_name: 2023_NatureComm_Schmid.pdf
file_size: 1786475
relation: main_file
success: 1
file_date_updated: 2023-04-25T09:13:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative assessment can stabilize indirect reciprocity under imperfect
information
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12862'
abstract:
- lang: eng
text: Despite the considerable progress of in vivo neural recording techniques,
inferring the biophysical mechanisms underlying large scale coordination of brain
activity from neural data remains challenging. One obstacle is the difficulty
to link high dimensional functional connectivity measures to mechanistic models
of network activity. We address this issue by investigating spike-field coupling
(SFC) measurements, which quantify the synchronization between, on the one hand,
the action potentials produced by neurons, and on the other hand mesoscopic “field”
signals, reflecting subthreshold activities at possibly multiple recording sites.
As the number of recording sites gets large, the amount of pairwise SFC measurements
becomes overwhelmingly challenging to interpret. We develop Generalized Phase
Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate
SFC. GPLA describes the dominant coupling between field activity and neural ensembles
across space and frequencies. We show that GPLA features are biophysically interpretable
when used in conjunction with appropriate network models, such that we can identify
the influence of underlying circuit properties on these features. We demonstrate
the statistical benefits and interpretability of this approach in various computational
models and Utah array recordings. The results suggest that GPLA, used jointly
with biophysical modeling, can help uncover the contribution of recurrent microcircuits
to the spatio-temporal dynamics observed in multi-channel experimental recordings.
acknowledgement: "We thank Britni Crocker for help with preprocessing of the data
and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support;
Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll
authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal
Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe
Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from
the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02).
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript. "
article_number: e1010983
article_processing_charge: No
article_type: original
author:
- first_name: Shervin
full_name: Safavi, Shervin
last_name: Safavi
- first_name: Theofanis I.
full_name: Panagiotaropoulos, Theofanis I.
last_name: Panagiotaropoulos
- first_name: Vishal
full_name: Kapoor, Vishal
last_name: Kapoor
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
citation:
ama: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK,
Besserve M. Uncovering the organization of neural circuits with Generalized Phase
Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983
apa: Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F.,
Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural
circuits with Generalized Phase Locking Analysis. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983
chicago: Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F
Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization
of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational
Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.
ieee: S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N.
K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits
with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol.
19, no. 4. Public Library of Science, 2023.
ista: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis
NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized
Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.
mla: Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with
Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19,
no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.
short: S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K.
Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-01T14:15:16Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pcbi.1010983
external_id:
isi:
- '000962668700002'
file:
- access_level: open_access
checksum: edeb9d09f3e41ba7c0251308b9e372e7
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T08:59:18Z
date_updated: 2023-04-25T08:59:18Z
file_id: '12867'
file_name: 2023_PLoSCompBio_Safavi.pdf
file_size: 4737671
relation: main_file
success: 1
file_date_updated: 2023-04-25T08:59:18Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/shervinsafavi/gpla.git
scopus_import: '1'
status: public
title: Uncovering the organization of neural circuits with Generalized Phase Locking
Analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '12879'
abstract:
- lang: eng
text: Machine learning (ML) has been widely applied to chemical property prediction,
most prominently for the energies and forces in molecules and materials. The strong
interest in predicting energies in particular has led to a ‘local energy’-based
paradigm for modern atomistic ML models, which ensures size-extensivity and a
linear scaling of computational cost with system size. However, many electronic
properties (such as excitation energies or ionization energies) do not necessarily
scale linearly with system size and may even be spatially localized. Using size-extensive
models in these cases can lead to large errors. In this work, we explore different
strategies for learning intensive and localized properties, using HOMO energies
in organic molecules as a representative test case. In particular, we analyze
the pooling functions that atomistic neural networks use to predict molecular
properties, and suggest an orbital weighted average (OWA) approach that enables
the accurate prediction of orbital energies and locations.
acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is
grateful for the TUM graduate school finance support to visit Bingqing Cheng's group
in IST for two months. We also thankfully acknowledge computational resources provided
by the MPCDF Supercomputing Centre.
article_processing_charge: No
article_type: original
author:
- first_name: Ke
full_name: Chen, Ke
id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d
last_name: Chen
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
citation:
ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning
of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j
apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired
machine learning of localized intensive properties. Chemical Science. Royal
Society of Chemistry. https://doi.org/10.1039/d3sc00841j
chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes
T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.”
Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.
ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired
machine learning of localized intensive properties,” Chemical Science.
Royal Society of Chemistry, 2023.
ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine
learning of localized intensive properties. Chemical Science.
mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive
Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.
short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:18:10Z
day: '10'
ddc:
- '000'
- '540'
department:
- _id: BiCh
doi: 10.1039/d3sc00841j
external_id:
isi:
- '000971508100001'
file:
- access_level: open_access
checksum: 5eeec69a51e192dcd94b955d84423836
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:17:05Z
date_updated: 2023-05-02T07:17:05Z
file_id: '12883'
file_name: 2023_ChemialScience_Chen.pdf
file_size: 1515446
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:17:05Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics-inspired machine learning of localized intensive properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12876'
abstract:
- lang: eng
text: "Motivation: The problem of model inference is of fundamental importance to
systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally
attractive approach capable of handling large biological networks. The models
are typically inferred from experimental data. However, even with a substantial
amount of experimental data supported by some prior knowledge, existing inference
methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults:
We propose Boolean network sketches as a new formal instrument for the inference
of Boolean networks. A sketch integrates (typically partial) knowledge about the
network’s topology and the update logic (obtained through, e.g. a biological knowledge
base or a literature search), as well as further assumptions about the properties
of the network’s transitions (e.g. the form of its attractor landscape), and additional
restrictions on the model dynamics given by the measured experimental data. Our
new BNs inference algorithm starts with an ‘initial’ sketch, which is extended
by adding restrictions representing experimental data to a ‘data-informed’ sketch
and subsequently computes all BNs consistent with the data-informed sketch. Our
algorithm is based on a symbolic representation and coloured model-checking. Our
approach is unique in its ability to cover a broad spectrum of knowledge and efficiently
produce a compact representation of all inferred BNs. We evaluate the method on
a non-trivial collection of real-world and simulated data."
acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S];
and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was
partially supported by European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].
article_number: btad158
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Ondřej
full_name: Huvar, Ondřej
last_name: Huvar
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
citation:
ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 2023;39(4).
doi:10.1093/bioinformatics/btad158'
apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean
network sketches: A unifying framework for logical model inference. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158'
chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek.
“Boolean Network Sketches: A Unifying Framework for Logical Model Inference.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.'
ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network
sketches: A unifying framework for logical model inference,” Bioinformatics,
vol. 39, no. 4. Oxford Academic, 2023.'
ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.'
mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for
Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford
Academic, 2023, doi:10.1093/bioinformatics/btad158.'
short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).
date_created: 2023-04-30T22:01:05Z
date_published: 2023-04-03T00:00:00Z
date_updated: 2023-08-01T14:27:28Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad158
ec_funded: 1
external_id:
isi:
- '000976610800001'
pmid:
- '37004199'
file:
- access_level: open_access
checksum: 2cb90ddf781baefddf47eac4b54e2a03
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:39:04Z
date_updated: 2023-05-02T07:39:04Z
file_id: '12886'
file_name: 2023_Bioinformatics_Benes.pdf
file_size: 478740
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:39:04Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.7688740
scopus_import: '1'
status: public
title: 'Boolean network sketches: A unifying framework for logical model inference'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2023'
...
---
_id: '12880'
abstract:
- lang: eng
text: Peripheral heterochromatin positioning depends on nuclear envelope associated
proteins and repressive histone modifications. Here we show that overexpression
(OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin
into heterochromatic foci within the nucleoplasm. These changes represent a perturbation
of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent
from altering other heterochromatin anchors or histone post-translational modifications.
We further show that LmnB1 OE alters gene expression. These changes do not correlate
with different levels of H3K9me3, but a significant number of the misregulated
genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed
an enrichment of developmental processes amongst the upregulated genes. ~74% of
these genes were normally repressed in our cell type, suggesting that LmnB1 OE
promotes gene de-repression. This demonstrates a broader consequence of LmnB1
OE on cell fate, and highlights the importance of maintaining proper levels of
LmnB1.
acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript;
Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing
Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195,
the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run
libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute,
with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg
Initiative Imaging Scientist Award, for electron microscopy sample preparation and
imaging.'
article_number: '2202548'
article_processing_charge: No
article_type: original
author:
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin
organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548
apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression
alters chromatin organization and gene expression. Nucleus. Taylor &
Francis. https://doi.org/10.1080/19491034.2023.2202548
chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1
Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus.
Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.
ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression
alters chromatin organization and gene expression,” Nucleus, vol. 14, no.
1. Taylor & Francis, 2023.
ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters
chromatin organization and gene expression. Nucleus. 14(1), 2202548.
mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization
and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis,
2023, doi:10.1080/19491034.2023.2202548.
short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:18:46Z
day: '18'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1080/19491034.2023.2202548
external_id:
isi:
- '000971629400001'
pmid:
- '37071033'
file:
- access_level: open_access
checksum: 8e707eda84f64dbad7f03545ae0a83ef
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:24:55Z
date_updated: 2023-05-02T07:24:55Z
file_id: '12884'
file_name: 2023_Nucleus_Kaneshiro.pdf
file_size: 3811113
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:24:55Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleus
publication_identifier:
eissn:
- 1949-1042
issn:
- 1949-1034
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamin B1 overexpression alters chromatin organization and gene expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12914'
abstract:
- lang: eng
text: We numerically study two methods of measuring tunneling times using a quantum
clock. In the conventional method using the Larmor clock, we show that the Larmor
tunneling time can be shorter for higher tunneling barriers. In the second method,
we study the probability of a spin-flip of a particle when it is transmitted through
a potential barrier including a spatially rotating field interacting with its
spin. According to the adiabatic theorem, the probability depends on the velocity
of the particle inside the barrier. It is numerically observed that the probability
increases for higher barriers, which is consistent with the result obtained by
the Larmor clock. By comparing outcomes for different initial spin states, we
suggest that one of the main causes of the apparent decrease in the tunneling
time can be the filtering effect occurring at the end of the barrier.
acknowledgement: We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C.
H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos
National Laboratory LDRD program under Project No. 20230049DR and the Center for
Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and
innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support.
W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the
Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support
while this work was being done.
article_number: '042216'
article_processing_charge: No
article_type: original
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: William G.
full_name: Unruh, William G.
last_name: Unruh
citation:
ama: Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling
times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216
apa: Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations
for measuring tunneling times. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.107.042216
chicago: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A. American Physical Society,
2023. https://doi.org/10.1103/PhysRevA.107.042216.
ieee: F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring
tunneling times,” Physical Review A, vol. 107, no. 4. American Physical
Society, 2023.
ista: Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring
tunneling times. Physical Review A. 107(4), 042216.
mla: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216,
American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.
short: F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-08-01T14:33:21Z
day: '20'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.107.042216
ec_funded: 1
external_id:
arxiv:
- '2207.13130'
isi:
- '000975799300006'
intvolume: ' 107'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2207.13130
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Numerical quantum clock simulations for measuring tunneling times
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12913'
abstract:
- lang: eng
text: The coexistence of gate-tunable superconducting, magnetic and topological
orders in magic-angle twisted bilayer graphene provides opportunities for the
creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined
symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where
the weak link is gate-tuned close to the correlated insulator state with a moiré
filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer
pattern with a pronounced magnetic hysteresis. Our theoretical calculations of
the junction weak link—with valley polarization and orbital magnetization—explain
most of these unconventional features. The effects persist up to the critical
temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show
how the combination of magnetization and its current-induced magnetization switching
allows us to realise a programmable zero-field superconducting diode. Our results
represent a major advance towards the creation of future superconducting quantum
electronic devices.
acknowledgement: We are grateful for the fruitful discussions with Allan MacDonald
and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and
Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence
in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat
de Catalunya through the CERCA program, funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support
of the Ministry of Science and Technology of China and the HKRGC through grants
MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support
from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021).
Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.
article_number: '2396'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Díez-Mérida, J.
last_name: Díez-Mérida
- first_name: A.
full_name: Díez-Carlón, A.
last_name: Díez-Carlón
- first_name: S. Y.
full_name: Yang, S. Y.
last_name: Yang
- first_name: Y. M.
full_name: Xie, Y. M.
last_name: Xie
- first_name: X. J.
full_name: Gao, X. J.
last_name: Gao
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: X.
full_name: Lu, X.
last_name: Lu
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: K. T.
full_name: Law, K. T.
last_name: Law
- first_name: Dmitri K.
full_name: Efetov, Dmitri K.
last_name: Efetov
citation:
ama: Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions
and superconducting diodes in magic-angle twisted bilayer graphene. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38005-7
apa: Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior,
J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-38005-7
chicago: Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden
L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.
ieee: J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe
K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken
Josephson junctions and superconducting diodes in magic-angle twisted bilayer
graphene. Nature Communications. 14, 2396.
mla: Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications,
vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.
short: J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior,
K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature
Communications 14 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-08-01T14:34:00Z
day: '26'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.1038/s41467-023-38005-7
external_id:
isi:
- '000979744000004'
pmid:
- '37100775'
file:
- access_level: open_access
checksum: a778105665c10beb2354c92d2b295115
content_type: application/pdf
creator: dernst
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file_name: 2023_NatureComm_DiezMerida.pdf
file_size: 1405588
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file_date_updated: 2023-05-08T07:26:40Z
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isi: 1
language:
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month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-broken Josephson junctions and superconducting diodes in magic-angle
twisted bilayer graphene
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '10550'
abstract:
- lang: eng
text: The global existence of renormalised solutions and convergence to equilibrium
for reaction-diffusion systems with non-linear diffusion are investigated. The
system is assumed to have quasi-positive non-linearities and to satisfy an entropy
inequality. The difficulties in establishing global renormalised solutions caused
by possibly degenerate diffusion are overcome by introducing a new class of weighted
truncation functions. By means of the obtained global renormalised solutions,
we study the large-time behaviour of complex balanced systems arising from chemical
reaction network theory with non-linear diffusion. When the reaction network does
not admit boundary equilibria, the complex balanced equilibrium is shown, by using
the entropy method, to exponentially attract all renormalised solutions in the
same compatibility class. This convergence extends even to a range of non-linear
diffusion, where global existence is an open problem, yet we are able to show
that solutions to approximate systems converge exponentially to equilibrium uniformly
in the regularisation parameter.
acknowledgement: "We thank the referees for their valuable comments and suggestions.
A major part of this work was carried out when B. Q. Tang visited the Institute
of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged.
This work was partially supported by NAWI Graz.\r\nOpen access funding provided
by University of Graz."
article_number: '66'
article_processing_charge: No
article_type: original
author:
- first_name: Klemens
full_name: Fellner, Klemens
last_name: Fellner
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
- first_name: Bao Quoc
full_name: Tang, Bao Quoc
last_name: Tang
citation:
ama: Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and
equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w
apa: Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion.
Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w
chicago: Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang.
“Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems
with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature,
2023. https://doi.org/10.1007/s00332-023-09926-w.
ieee: K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion,”
Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.
ista: Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions
and equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 33, 66.
mla: Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of
Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear
Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.
short: K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science
33 (2023).
date_created: 2021-12-16T12:15:35Z
date_published: 2023-06-07T00:00:00Z
date_updated: 2023-08-01T14:40:33Z
day: '07'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00332-023-09926-w
external_id:
arxiv:
- '2109.12019'
isi:
- '001002343400002'
file:
- access_level: open_access
checksum: f3f0f0886098e31c81116cff8183750b
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T07:33:53Z
date_updated: 2023-06-19T07:33:53Z
file_id: '13149'
file_name: 2023_JourNonlinearScience_Fellner.pdf
file_size: 742315
relation: main_file
success: 1
file_date_updated: 2023-06-19T07:33:53Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Journal of Nonlinear Science
publication_identifier:
eissn:
- 1432-1467
issn:
- 0938-8974
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global renormalised solutions and equilibration of reaction-diffusion systems
with non-linear diffusion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2023'
...
---
_id: '13043'
abstract:
- lang: eng
text: "We derive a weak-strong uniqueness principle for BV solutions to multiphase
mean curvature flow of triple line clusters in three dimensions. Our proof is
based on the explicit construction\r\nof a gradient flow calibration in the sense
of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends
the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting
along triple junctions."
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Tim
full_name: Laux, Tim
last_name: Laux
citation:
ama: Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double
bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484
apa: Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature
flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484
chicago: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature
Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023.
https://doi.org/10.4171/IFB/484.
ieee: S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow
of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS
Press, pp. 37–107, 2023.
ista: Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow
of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.
mla: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature
Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1,
EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.
short: S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.
date_created: 2023-05-21T22:01:06Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-08-01T14:43:29Z
day: '20'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.4171/IFB/484
ec_funded: 1
external_id:
arxiv:
- '2108.01733'
isi:
- '000975817300002'
file:
- access_level: open_access
checksum: 622422484810441e48f613e968c7e7a4
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:24:13Z
date_updated: 2023-05-22T07:24:13Z
file_id: '13045'
file_name: 2023_Interfaces_Hensel.pdf
file_size: 867876
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:24:13Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 37-107
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Interfaces and Free Boundaries
publication_identifier:
eissn:
- 1463-9971
issn:
- 1463-9963
publication_status: published
publisher: EMS Press
quality_controlled: '1'
related_material:
record:
- id: '10013'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Weak-strong uniqueness for the mean curvature flow of double bubbles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2023'
...
---
_id: '12912'
abstract:
- lang: eng
text: The chemical potential of adsorbed or confined fluids provides insight into
their unique thermodynamic properties and determines adsorption isotherms. However,
it is often difficult to compute this quantity from atomistic simulations using
existing statistical mechanical methods. We introduce a computational framework
that utilizes static structure factors, thermodynamic integration, and free energy
perturbation for calculating the absolute chemical potential of fluids. For demonstration,
we apply the method to compute the adsorption isotherms of carbon dioxide in a
metal-organic framework and water in carbon nanotubes.
acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments
and suggestions on the article. B.C. acknowledges the resources provided by the
Cambridge Tier-2 system operated by the University of Cambridge Research Computing
Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.
article_number: '161101 '
article_processing_charge: No
article_type: original
author:
- first_name: Rochus
full_name: Schmid, Rochus
last_name: Schmid
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids.
The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711
apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed
or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711
chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023.
https://doi.org/10.1063/5.0146711.
ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined
fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing,
2023.
ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined
fluids. The Journal of Chemical Physics. 158(16), 161101.
mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16,
161101, AIP Publishing, 2023, doi:10.1063/5.0146711.
short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-24T00:00:00Z
date_updated: 2023-08-01T14:34:49Z
day: '24'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0146711
external_id:
arxiv:
- '2302.01297'
isi:
- '001010676000010'
pmid:
- '37093149'
file:
- access_level: open_access
checksum: 4ab8c965f2fa4e17920bfa846847f137
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:44:49Z
date_updated: 2023-05-08T07:44:49Z
file_id: '12918'
file_name: 2023_JourChemicalPhysics_Schmid.pdf
file_size: 6499468
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:44:49Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/mu-adsorption
- relation: software
url: https://github.com/BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of adsorbed or confined fluids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2023'
...
---
_id: '12972'
abstract:
- lang: eng
text: Embroidery is a long-standing and high-quality approach to making logos and
images on textiles. Nowadays, it can also be performed via automated machines
that weave threads with high spatial accuracy. A characteristic feature of the
appearance of the threads is a high degree of anisotropy. The anisotropic behavior
is caused by depositing thin but long strings of thread. As a result, the stitched
patterns convey both color and direction. Artists leverage this anisotropic behavior
to enhance pure color images with textures, illusions of motion, or depth cues.
However, designing colorful embroidery patterns with prescribed directionality
is a challenging task, one usually requiring an expert designer. In this work,
we propose an interactive algorithm that generates machine-fabricable embroidery
patterns from multi-chromatic images equipped with user-specified directionality
fields.We cast the problem of finding a stitching pattern into vector theory.
To find a suitable stitching pattern, we extract sources and sinks from the divergence
field of the vector field extracted from the input and use them to trace streamlines.
We further optimize the streamlines to guarantee a smooth and connected stitching
pattern. The generated patterns approximate the color distribution constrained
by the directionality field. To allow for further artistic control, the trade-off
between color match and directionality match can be interactively explored via
an intuitive slider. We showcase our approach by fabricating several embroidery
paths.
acknowledgement: This work was supported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program (grant agreement
No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous
reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and
Paola Mejia for proofreading; everyone in the visual computing group at ISTA for
inspiring lunch and coffee breaks; Thibault Tricard for help producing the results
of Phasor Noise.
article_processing_charge: No
article_type: original
author:
- first_name: Zhenyuan
full_name: Liu, Zhenyuan
id: 70f0d7cf-ae65-11ec-a14f-89dfc5505b19
last_name: Liu
orcid: 0000-0001-9200-5690
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Raphael
full_name: Charrondiere, Raphael
id: a3a24133-2cc7-11ec-be88-8ddaf6f464b1
last_name: Charrondiere
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware
design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409.
doi:10.1111/cgf.14770
apa: 'Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023).
Directionality-aware design of embroidery patterns. Computer Graphics Forum.
Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770
'
chicago: Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere,
and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer
Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770
.
ieee: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware
design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2.
Wiley, pp. 397–409, 2023.
ista: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware
design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409.
mla: Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.”
Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .
short: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics
Forum 42 (2023) 397–409.
conference:
end_date: 2023-05-12
location: Saarbrucken, Germany
name: 'EG: Eurographics'
start_date: 2023-05-08
date_created: 2023-05-16T08:47:25Z
date_published: 2023-05-08T00:00:00Z
date_updated: 2023-08-01T14:47:05Z
day: '08'
ddc:
- '004'
department:
- _id: BeBi
doi: '10.1111/cgf.14770 '
ec_funded: 1
external_id:
isi:
- '001000062600033'
file:
- access_level: open_access
checksum: 4c188c2be4745467a8790bbf5d6491aa
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T08:28:37Z
date_updated: 2023-05-16T08:28:37Z
file_id: '12974'
file_name: Zhenyuan2023.pdf
file_size: 24003702
relation: main_file
success: 1
file_date_updated: 2023-05-16T08:28:37Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '2'
keyword:
- embroidery
- design
- directionality
- density
- image
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 397-409
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics Forum
publication_identifier:
issn:
- 1467-8659
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Directionality-aware design of embroidery patterns
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 42
year: '2023'
...
---
_id: '13033'
abstract:
- lang: eng
text: Current methods for assessing cell proliferation in 3D scaffolds rely on changes
in metabolic activity or total DNA, however, direct quantification of cell number
in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased
stereology approach that uses systematic-random sampling and thin focal-plane
optical sectioning of the scaffolds followed by estimation of total cell number
(StereoCount). This approach was validated against an indirect method for measuring
the total DNA (DNA content); and the Bürker counting chamber, the current reference
method for quantifying cell number. We assessed the total cell number for cell
seeding density (cells per unit volume) across four values and compared the methods
in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount
markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold.
For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA
content showed lower accuracy than the Bürker but did not differ from each other.
In terms of ease-of-use, there was a strong advantage for the StereoCount due
to output in terms of absolute cell numbers along with the possibility for an
overview of cell distribution and future use of automation for high throughput
analysis. Taking together, the StereoCount method is an efficient approach for
direct cell quantification in 3D collagen scaffolds. Its major benefit is that
automated StereoCount could accelerate research using 3D scaffolds focused on
drug discovery for a wide variety of human diseases.
acknowledgement: The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787
“Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the
Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE
project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein
and Norway through the EEA Grants and the Technology Agency of the Czech Republic
and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation
(U.S. Public Health Service). The authors acknowledge the invaluable assistance
provided by Iveta Paurova via her support in terms of the provision of laboratory
services.
article_number: '7959'
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Zavadakova, Anna
last_name: Zavadakova
- first_name: Lucie
full_name: Vistejnova, Lucie
last_name: Vistejnova
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Filip
full_name: Tichanek, Filip
last_name: Tichanek
- first_name: Dagmar
full_name: Bilikova, Dagmar
last_name: Bilikova
- first_name: Peter R.
full_name: Mouton, Peter R.
last_name: Mouton
citation:
ama: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
Novel stereological method for estimation of cell counts in 3D collagen scaffolds.
Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z
apa: Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &
Mouton, P. R. (2023). Novel stereological method for estimation of cell counts
in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z
chicago: Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar
Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature,
2023. https://doi.org/10.1038/s41598-023-35162-z.
ieee: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P.
R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen
scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.
ista: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
2023. Novel stereological method for estimation of cell counts in 3D collagen
scaffolds. Scientific Reports. 13(1), 7959.
mla: Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959,
Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.
short: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R.
Mouton, Scientific Reports 13 (2023).
date_created: 2023-05-19T11:12:25Z
date_published: 2023-05-17T00:00:00Z
date_updated: 2023-08-01T14:46:06Z
day: '17'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1038/s41598-023-35162-z
external_id:
isi:
- '000995271600104'
file:
- access_level: open_access
checksum: 8c1b769693ff4288df8376e59ad1176d
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:57:37Z
date_updated: 2023-05-22T07:57:37Z
file_id: '13047'
file_name: 2023_ScientificReports_Zavadakova.pdf
file_size: 3055077
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:57:37Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41598-023-37265-z
scopus_import: '1'
status: public
title: Novel stereological method for estimation of cell counts in 3D collagen scaffolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '13095'
abstract:
- lang: eng
text: Disulfide bond formation is fundamentally important for protein structure
and constitutes a key mechanism by which cells regulate the intracellular oxidation
state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen
peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally,
upon Cys oxidation PRDXs undergo extensive conformational rearrangements that
may underlie their presently structurally poorly defined functions as molecular
chaperones. Rearrangements include high molecular-weight oligomerization, the
dynamics of which are, however, poorly understood, as is the impact of disulfide
bond formation on these properties. Here we show that formation of disulfide bonds
along the catalytic cycle induces extensive μs time scale dynamics, as monitored
by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR
of a designed dimeric mutant. We ascribe the conformational dynamics to structural
frustration, resulting from conflicts between the disulfide-constrained reduction
of mobility and the desire to fulfill other favorable contacts.
acknowledgement: "We thank Albert A. Smith (Univ. Leipzig) for discussions and help
with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments
(Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis
script. Intramural funding from Institute of Science and Technology Austria is acknowledged.
This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG;
UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology
(PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both
platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges
funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish
Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through
a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre
for Molecular and Translational Medicine, University of Gothenburg, Sweden. "
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Troussicot, Laura
id: 3d9cac31-413c-11eb-9514-d1ec2a7fb7f3
last_name: Troussicot
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Mikael
full_name: Molin, Mikael
last_name: Molin
- first_name: Björn M.
full_name: Burmann, Björn M.
last_name: Burmann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal
of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200
apa: Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023).
Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin
from MAS NMR. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.3c01200
chicago: Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul
Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in
a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society.
American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.
ieee: L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,”
Journal of the American Chemical Society, vol. 145, no. 19. American Chemical
Society, pp. 10700–10711, 2023.
ista: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal
of the American Chemical Society. 145(19), 10700–10711.
mla: Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and
Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American
Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711,
doi:10.1021/jacs.3c01200.
short: L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of
the American Chemical Society 145 (2023) 10700–10711.
date_created: 2023-05-28T22:01:04Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:48:09Z
day: '04'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1021/jacs.3c01200
external_id:
isi:
- '000985907400001'
pmid:
- '37140345'
file:
- access_level: open_access
checksum: 0758a930ef21c62fc91b14e657479f83
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:05:28Z
date_updated: 2023-05-30T07:05:28Z
file_id: '13098'
file_name: 2023_JACS_Troussicot.pdf
file_size: 6719299
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:05:28Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 10700–10711
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '12820'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin
from MAS NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 145
year: '2023'
...
---
_id: '13042'
abstract:
- lang: eng
text: Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We
show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for
c>20, thus extending a result of Frieze and the author to smaller values of
c. Thereafter, for c>20, we determine the limit of the probability that
G(n, c/n)contains cycles of every length between the length of its shortest and its longest
cycles as n→∞.
acknowledgement: We would like to thank the reviewers for their helpful comments and
remarks.
article_number: P2.21
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: Anastos M. A note on long cycles in sparse random graphs. Electronic Journal
of Combinatorics. 2023;30(2). doi:10.37236/11471
apa: Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471
chicago: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471.
ieee: M. Anastos, “A note on long cycles in sparse random graphs,” Electronic
Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics,
2023.
ista: Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic
Journal of Combinatorics. 30(2), P2.21.
mla: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic
Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics,
2023, doi:10.37236/11471.
short: M. Anastos, Electronic Journal of Combinatorics 30 (2023).
date_created: 2023-05-21T22:01:05Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-01T14:44:52Z
day: '05'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11471
external_id:
arxiv:
- '2105.13828'
isi:
- '000988285500001'
file:
- access_level: open_access
checksum: 6269ed3b3eded6536d3d9d6baad2d5b9
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:43:19Z
date_updated: 2023-05-22T07:43:19Z
file_id: '13046'
file_name: 2023_JourCombinatorics_Anastos.pdf
file_size: 448736
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:43:19Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on long cycles in sparse random graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2023'
...
---
_id: '12820'
abstract:
- lang: eng
text: "Disulfide bond formation is fundamentally important for protein structure,
and constitutes a key mechanism by which cells regulate the intracellular oxidation
state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen
peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally,
upon Cys oxidation PRDXs undergo extensive conformational rearrangements that
may underlie their presently structurally poorly defined functions as molecular
chaperones. Rearrangements include high molecular-weight oligomerization, the
dynamics of which are, however, poorly understood, as is the impact of disulfide
bond formation on these properties. Here we show that formation of disulfide bonds
along the catalytic cycle induces extensive microsecond time scale dynamics, as
monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly
and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics
to structural frustration, resulting from conflicts between the disulfide-constrained
reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis
data repository contains NMR data presented in the associated manuscript"
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Research data of the publication “Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820
apa: Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820
chicago: Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.
ieee: P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute
of Science and Technology Austria, 2023.
ista: Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.
mla: Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.
short: P. Schanda, (2023).
contributor:
- contributor_type: researcher
first_name: Laura
last_name: Troussicot
- contributor_type: researcher
first_name: Björn M.
last_name: Burmann
date_created: 2023-04-10T05:55:56Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:48:08Z
day: '18'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.15479/AT:ISTA:12820
file:
- access_level: open_access
checksum: 54a619605e44c871214fb0e07b05c6bf
content_type: application/zip
creator: pschanda
date_created: 2023-04-14T09:39:33Z
date_updated: 2023-04-14T09:39:33Z
file_id: '12823'
file_name: data_deposition.zip
file_size: 54184807
relation: main_file
success: 1
- access_level: open_access
checksum: 8dede9fc78399d13144eb05c62bf5750
content_type: application/octet-stream
creator: pschanda
date_created: 2023-04-14T09:39:58Z
date_updated: 2023-04-14T09:39:58Z
file_id: '12824'
file_name: README
file_size: 4978
relation: main_file
success: 1
file_date_updated: 2023-04-14T09:39:58Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13095'
relation: used_in_publication
status: public
status: public
title: Research data of the publication "Disulfide-bond-induced structural frustration
and dynamic disorder in a peroxiredoxin from MAS NMR"
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13092'
abstract:
- lang: eng
text: There is a need for the development of lead-free thermoelectric materials
for medium-/high-temperature applications. Here, we report a thiol-free tin telluride
(SnTe) precursor that can be thermally decomposed to produce SnTe crystals with
sizes ranging from tens to several hundreds of nanometers. We further engineer
SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing
the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles.
The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase
effectively improves the electrical conductivity of SnTe while simultaneously
reducing the lattice thermal conductivity without compromising the Seebeck coefficient.
Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit
up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared
with pristine SnTe.
acknowledgement: Open Access is funded by the Austrian Science Fund (FWF). We thank
Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X.,
and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support.
C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement
M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan
Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute
of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial
support from IST Austria.
article_processing_charge: No
article_type: original
author:
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Xuan
full_name: Song, Xuan
last_name: Song
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Linlin
full_name: Yang, Linlin
last_name: Yang
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric
composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389.
doi:10.1021/acsami.3c00625
apa: Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023).
Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials
and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625
chicago: Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona
Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS
Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625.
ieee: B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,”
ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical
Society, pp. 23380–23389, 2023.
ista: Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez
M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites.
ACS Applied Materials and Interfaces. 15(19), 23380–23389.
mla: Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.”
ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical
Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625.
short: B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H.
Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:50:09Z
day: '04'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsami.3c00625
external_id:
isi:
- '000985497900001'
pmid:
- '37141543'
file:
- access_level: open_access
checksum: 23893be46763c4c78daacddd019de821
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:38:44Z
date_updated: 2023-05-30T07:38:44Z
file_id: '13099'
file_name: 2023_ACSAppliedMaterials_Nan.pdf
file_size: 5640829
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:38:44Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 23380–23389
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bottom-up synthesis of SnTe-based thermoelectric composites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2023'
...
---
_id: '13094'
abstract:
- lang: eng
text: 'Endocytosis is a key cellular process involved in the uptake of nutrients,
pathogens, or the therapy of diseases. Most studies have focused on spherical
objects, whereas biologically relevant shapes can be highly anisotropic. In this
letter, we use an experimental model system based on Giant Unilamellar Vesicles
(GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first
stage of the passive endocytic process: engulfment of an anisotropic object by
the membrane. Our model has specific ligand–receptor interactions realized by
mobile receptors on the vesicles and immobile ligands on the particles. Through
a series of experiments, theory, and molecular dynamics simulations, we quantify
the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages
of the wrapping pathway. We find that the strong curvature variation in the neck
of the dumbbell as well as membrane tension are crucial in determining both the
speed of wrapping and the final states.'
acknowledgement: We sincerely thank Casper van der Wel for providing open-source packages
for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation
and Rachel Doherty for her assistance with particle functionalization. We are grateful
to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and
A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation
programme (ERC Starting Grant No. 802960).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ali
full_name: Azadbakht, Ali
last_name: Azadbakht
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
- first_name: Thijs
full_name: Varkevisser, Thijs
last_name: Varkevisser
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways
of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters.
2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375
apa: Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D.
J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar
Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375
chicago: Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and
Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant
Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.
ieee: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano
Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.
ista: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano
Letters. 23(10), 4267–4273.
mla: Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles
by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American
Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.
short: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano
Letters 23 (2023) 4267–4273.
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:51:25Z
day: '04'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1021/acs.nanolett.3c00375
ec_funded: 1
external_id:
isi:
- '000985481400001'
pmid:
- '37141427'
file:
- access_level: open_access
checksum: 9734d4c617bab3578ef62916b764547a
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:55:31Z
date_updated: 2023-05-30T07:55:31Z
file_id: '13100'
file_name: 2023_NanoLetters_Azadbakht.pdf
file_size: 3654910
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:55:31Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4267–4273
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2023'
...
---
_id: '13093'
abstract:
- lang: eng
text: The direct, solid state, and reversible conversion between heat and electricity
using thermoelectric devices finds numerous potential uses, especially around
room temperature. However, the relatively high material processing cost limits
their real applications. Silver selenide (Ag2Se) is one of the very few n-type
thermoelectric (TE) materials for room-temperature applications. Herein, we report
a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se,
which can be extended to other metal chalcogenides. These materials reach TE figures
of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide
(Bi2S3) particles also prepared in an aqueous solution are incorporated into the
Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt %
of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering.
The presence of Bi2S3 significantly improves the Seebeck coefficient and power
factor while at the same time decreasing the thermal conductivity with no apparent
drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved
in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT
value (zTave) of 0.93 in the 300–390 K range is demonstrated.
acknowledgement: 'Open Access is funded by the Austrian Science Fund (FWF). B.N.,
M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship
support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement
M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens
Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457
and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/.
ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.:
CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya.
J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and
projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges
support from the National Natural Science Foundation of China (22208293). This study
is part of the Advanced Materials programme and was supported by MCIN with funding
from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.'
article_processing_charge: No
article_type: original
author:
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Xu
full_name: Han, Xu
last_name: Han
- first_name: Yong
full_name: Zuo, Yong
last_name: Zuo
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based
on silver selenide in aqueous solution and ambient temperature. ACS Applied
Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055
apa: Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023).
Engineering of thermoelectric composites based on silver selenide in aqueous solution
and ambient temperature. ACS Applied Electronic Materials. American Chemical
Society. https://doi.org/10.1021/acsaelm.3c00055
chicago: Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang,
Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide
in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials.
American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055.
ieee: B. Nan et al., “Engineering of thermoelectric composites based on silver
selenide in aqueous solution and ambient temperature,” ACS Applied Electronic
Materials. American Chemical Society, 2023.
ista: Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol
J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites
based on silver selenide in aqueous solution and ambient temperature. ACS Applied
Electronic Materials.
mla: Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver
Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic
Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055.
short: B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J.
Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials
(2023).
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-01T14:50:48Z
day: '05'
department:
- _id: MaIb
doi: 10.1021/acsaelm.3c00055
external_id:
isi:
- '000986859000001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsaelm.3c00055
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: ACS Applied Electronic Materials
publication_identifier:
eissn:
- 2637-6113
publication_status: epub_ahead
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engineering of thermoelectric composites based on silver selenide in aqueous
solution and ambient temperature
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '13091'
abstract:
- lang: eng
text: We use a function field version of the Hardy–Littlewood circle method to study
the locus of free rational curves on an arbitrary smooth projective hypersurface
of sufficiently low degree. On the one hand this allows us to bound the dimension
of the singular locus of the moduli space of rational curves on such hypersurfaces
and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin
conjecture in terms of slopes with respect to the tangent bundle.
acknowledgement: The authors are grateful to Paul Nelson, Per Salberger and Jason
Starr for useful comments. While working on this paper the first author was supported
by EPRSC grant EP/P026710/1. The research was partially conducted during the period
the second author served as a Clay Research Fellow, and partially conducted during
the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and
the ETH Zurich Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Will
full_name: Sawin, Will
last_name: Sawin
citation:
ama: Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and
the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719
apa: Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree
hypersurfaces and the circle method. Algebra and Number Theory. Mathematical
Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719
chicago: Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree
Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical
Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719.
ieee: T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces
and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical
Sciences Publishers, pp. 719–748, 2023.
ista: Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces
and the circle method. Algebra and Number Theory. 17(3), 719–748.
mla: Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces
and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical
Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.
short: T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.
date_created: 2023-05-28T22:01:02Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2023-08-01T14:51:57Z
day: '12'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.2140/ant.2023.17.719
external_id:
arxiv:
- '1810.06882'
isi:
- '000996014700004'
file:
- access_level: open_access
checksum: 5d5d67b235905650e33cf7065d7583b4
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T08:05:22Z
date_updated: 2023-05-30T08:05:22Z
file_id: '13101'
file_name: 2023_AlgebraNumberTheory_Browning.pdf
file_size: 1430719
relation: main_file
success: 1
file_date_updated: 2023-05-30T08:05:22Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 719-748
project:
- _id: 26A8D266-B435-11E9-9278-68D0E5697425
grant_number: EP-P026710-2
name: Between rational and integral points
publication: Algebra and Number Theory
publication_identifier:
eissn:
- 1944-7833
issn:
- 1937-0652
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free rational curves on low degree hypersurfaces and the circle method
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2023'
...
---
_id: '13117'
abstract:
- lang: eng
text: The ability to control the direction of scattered light is crucial to provide
flexibility and scalability for a wide range of on-chip applications, such as
integrated photonics, quantum information processing, and nonlinear optics. Tunable
directionality can be achieved by applying external magnetic fields that modify
optical selection rules, by using nonlinear effects, or interactions with vibrations.
However, these approaches are less suitable to control microwave photon propagation
inside integrated superconducting quantum devices. Here, we demonstrate on-demand
tunable directional scattering based on two periodically modulated transmon qubits
coupled to a transmission line at a fixed distance. By changing the relative phase
between the modulation tones, we realize unidirectional forward or backward photon
scattering. Such an in-situ switchable mirror represents a versatile tool for
intra- and inter-chip microwave photonic processors. In the future, a lattice
of qubits can be used to realize topological circuits that exhibit strong nonreciprocity
or chirality.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski
for software development, and the MIBA workshop and the IST nanofabrication facility
for technical support. This work was supported by the Austrian Science Fund (FWF)
through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge
support from the European Research Council under grant agreement No 758053 (ERC
StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P.
has been supported by the Russian Science Foundation under the grant No 20-12-00194.
article_number: '2998'
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander V.
full_name: Poshakinskiy, Alexander V.
last_name: Poshakinskiy
- first_name: Riya
full_name: Sett, Riya
id: 2E6D040E-F248-11E8-B48F-1D18A9856A87
last_name: Sett
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Alexander N.
full_name: Poddubny, Alexander N.
last_name: Poddubny
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable
directional photon scattering from a pair of superconducting qubits. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38761-6
apa: Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N.,
& Fink, J. M. (2023). Tunable directional photon scattering from a pair of
superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6
chicago: Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka,
Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering
from a Pair of Superconducting Qubits.” Nature Communications. Springer
Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.
ieee: E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and
J. M. Fink, “Tunable directional photon scattering from a pair of superconducting
qubits,” Nature Communications, vol. 14. Springer Nature, 2023.
ista: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023.
Tunable directional photon scattering from a pair of superconducting qubits. Nature
Communications. 14, 2998.
mla: Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer
Nature, 2023, doi:10.1038/s41467-023-38761-6.
short: E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M.
Fink, Nature Communications 14 (2023).
date_created: 2023-06-04T22:01:02Z
date_published: 2023-05-24T00:00:00Z
date_updated: 2023-08-02T06:10:26Z
day: '24'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-023-38761-6
ec_funded: 1
external_id:
arxiv:
- '2205.03293'
isi:
- '001001099700002'
file:
- access_level: open_access
checksum: a857df40f0882859c48a1ff1e2001ec2
content_type: application/pdf
creator: dernst
date_created: 2023-06-06T07:31:20Z
date_updated: 2023-06-06T07:31:20Z
file_id: '13123'
file_name: 2023_NaturePhysics_Redchenko.pdf
file_size: 1654389
relation: main_file
success: 1
file_date_updated: 2023-06-06T07:31:20Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 26B354CA-B435-11E9-9278-68D0E5697425
name: Controllable Collective States of Superconducting Qubit Ensembles
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13124'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Tunable directional photon scattering from a pair of superconducting qubits
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '13106'
abstract:
- lang: eng
text: Quantum entanglement is a key resource in currently developed quantum technologies.
Sharing this fragile property between superconducting microwave circuits and optical
or atomic systems would enable new functionalities, but this has been hindered
by an energy scale mismatch of >104 and the resulting mutually imposed loss and
noise. In this work, we created and verified entanglement between microwave and
optical fields in a millikelvin environment. Using an optically pulsed superconducting
electro-optical device, we show entanglement between propagating microwave and
optical fields in the continuous variable domain. This achievement not only paves
the way for entanglement between superconducting circuits and telecom wavelength
light, but also has wide-ranging implications for hybrid quantum networks in the
context of modularization, scaling, sensing, and cross-platform verification.
acknowledgement: This work was supported by the European Research Council (grant no.
758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation
Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support
from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship
with funding from the European Union’s Horizon 2020 Research and Innovation Program
(Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support
from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European
Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen
QUARTET).
article_processing_charge: No
article_type: original
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
- first_name: Y.
full_name: Minoguchi, Y.
last_name: Minoguchi
- first_name: P.
full_name: Rabl, P.
last_name: Rabl
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science.
2023;380(6646):718-721. doi:10.1126/science.adg3812
apa: Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &
Fink, J. M. (2023). Entangling microwaves with light. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812
chicago: Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi,
P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science.
American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.
ieee: R. Sahu et al., “Entangling microwaves with light,” Science,
vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721,
2023.
ista: Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling
microwaves with light. Science. 380(6646), 718–721.
mla: Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol.
380, no. 6646, American Association for the Advancement of Science, 2023, pp.
718–21, doi:10.1126/science.adg3812.
short: R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink,
Science 380 (2023) 718–721.
date_created: 2023-05-31T11:39:24Z
date_published: 2023-05-18T00:00:00Z
date_updated: 2023-08-02T06:08:57Z
day: '18'
department:
- _id: JoFi
doi: 10.1126/science.adg3812
ec_funded: 1
external_id:
arxiv:
- '2301.03315'
isi:
- '000996515200004'
intvolume: ' 380'
isi: 1
issue: '6646'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.03315
month: '05'
oa: 1
oa_version: Preprint
page: 718-721
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/
record:
- id: '13122'
relation: research_data
status: public
status: public
title: Entangling microwaves with light
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 380
year: '2023'
...
---
_id: '13129'
abstract:
- lang: eng
text: "We study the representative volume element (RVE) method, which is a method
to approximately infer the effective behavior ahom of a stationary random medium.
The latter is described by a coefficient field a(x) generated from a given ensemble
⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory
of homogenization, the method proceeds by computing d=3 correctors (d denoting
the space dimension). To be numerically tractable, this computation has to be
done on a finite domain: the so-called representative volume element, i.e., a
large box with, say, periodic boundary conditions. The main message of this article
is: Periodize the ensemble instead of its realizations. By this, we mean that
it is better to sample from a suitably periodized ensemble than to periodically
extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩.
We make this point by investigating the bias (or systematic error), i.e., the
difference between ahom and the expected value of the RVE method, in terms of
its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x),
we heuristically argue that this error is generically O(L−1). In case of a suitable
periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give
a characterization of the leading-order error term for both strategies and argue
that even in the isotropic case it is generically non-degenerate. We carry out
the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian
type, which allow for a straightforward periodization, passing via the (integrable)
covariance function. This setting has also the advantage of making the Price theorem
and the Malliavin calculus available for optimal stochastic estimates of correctors.
We actually need control of second-order correctors to capture the leading-order
error term. This is due to inversion symmetry when applying the two-scale expansion
to the Green function. As a bonus, we present a stream-lined strategy to estimate
the error in a higher-order two-scale expansion of the Green function."
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nicolas
full_name: Clozeau, Nicolas
id: fea1b376-906f-11eb-847d-b2c0cf46455b
last_name: Clozeau
- first_name: Marc
full_name: Josien, Marc
last_name: Josien
- first_name: Felix
full_name: Otto, Felix
last_name: Otto
- first_name: Qiang
full_name: Xu, Qiang
last_name: Xu
citation:
ama: 'Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element
method: Periodize the ensemble instead of its realizations. Foundations of
Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y'
apa: 'Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative
volume element method: Periodize the ensemble instead of its realizations. Foundations
of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y'
chicago: 'Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the
Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.”
Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.'
ieee: 'N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume
element method: Periodize the ensemble instead of its realizations,” Foundations
of Computational Mathematics. Springer Nature, 2023.'
ista: 'Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume
element method: Periodize the ensemble instead of its realizations. Foundations
of Computational Mathematics.'
mla: 'Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method:
Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational
Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.'
short: N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics
(2023).
date_created: 2023-06-11T22:00:40Z
date_published: 2023-05-30T00:00:00Z
date_updated: 2023-08-02T06:12:39Z
day: '30'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s10208-023-09613-y
external_id:
isi:
- '000999623100001'
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10208-023-09613-y
month: '05'
oa: 1
oa_version: Published Version
publication: Foundations of Computational Mathematics
publication_identifier:
eissn:
- 1615-3383
issn:
- 1615-3375
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bias in the representative volume element method: Periodize the ensemble instead
of its realizations'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '13124'
abstract:
- lang: eng
text: This dataset comprises all data shown in the figures of the submitted article
"Tunable directional photon scattering from a pair of superconducting qubits"
at arXiv:2205.03293. Additional raw data are available from the corresponding
author on reasonable request.
article_processing_charge: No
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander
full_name: Poshakinskiy, Alexander
last_name: Poshakinskiy
- first_name: Riya
full_name: Sett, Riya
id: 2E6D040E-F248-11E8-B48F-1D18A9856A87
last_name: Sett
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Alexander
full_name: Poddubny, Alexander
last_name: Poddubny
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable
directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567
apa: Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &
Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting
qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567
chicago: Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander
Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.
ieee: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M.
Fink, “Tunable directional photon scattering from a pair of superconducting qubits.”
Zenodo, 2023.
ista: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023.
Tunable directional photon scattering from a pair of superconducting qubits, Zenodo,
10.5281/ZENODO.7858567.
mla: Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.
short: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink,
(2023).
date_created: 2023-06-06T07:36:50Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-08-02T06:10:25Z
day: '28'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.7858567
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.7858567
month: '04'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '13117'
relation: used_in_publication
status: public
status: public
title: Tunable directional photon scattering from a pair of superconducting qubits
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13122'
abstract:
- lang: eng
text: Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417
apa: Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417
chicago: Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.
ieee: R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.
ista: Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.
mla: Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417.
short: R. Sahu, (2023).
date_created: 2023-06-06T06:46:16Z
date_published: 2023-03-31T00:00:00Z
date_updated: 2023-08-02T06:08:56Z
day: '31'
department:
- _id: JoFi
doi: 10.5281/ZENODO.7789417
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.7789418
month: '03'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '13106'
relation: used_in_publication
status: public
status: public
title: Entangling microwaves with light
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13166'
abstract:
- lang: eng
text: Brachyury, a member of T-box gene family, is widely known for its major role
in mesoderm specification in bilaterians. It is also present in non-bilaterian
metazoans, such as cnidarians, where it acts as a component of an axial patterning
system. In this study, we present a phylogenetic analysis of Brachyury genes within
phylum Cnidaria, investigate differential expression and address a functional
framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates
two duplication events of Brachyury within the cnidarian lineage. The first duplication
likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans,
while the second duplication arose in the hydrozoan ancestor, resulting in three
copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern
marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3
expression was detected in scattered presumably nerve cells of the D. pumila larva.
Pharmacological modulations indicated that Brachyury3 is not under regulation
of cWnt signaling in contrast to the other two Brachyury genes. Divergence in
expression patterns and regulation suggest neofunctionalization of Brachyury3
in hydrozoans.
acknowledgement: "We thank N.A. Pertsov White Sea Biological Station of Moscow State
University for the help and support in obtaining samples and providing access to
all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We
are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork
in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under
the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy
(CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009
of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular
patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to
S.K.)."
article_number: '9382'
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra A.
full_name: Vetrova, Alexandra A.
last_name: Vetrova
- first_name: Daria M.
full_name: Kupaeva, Daria M.
last_name: Kupaeva
- first_name: Alena
full_name: Kizenko, Alena
id: a521c60b-0815-11ed-9b02-b8bd522477c8
last_name: Kizenko
- first_name: Tatiana S.
full_name: Lebedeva, Tatiana S.
last_name: Lebedeva
- first_name: Peter
full_name: Walentek, Peter
last_name: Walentek
- first_name: Nikoloz
full_name: Tsikolia, Nikoloz
last_name: Tsikolia
- first_name: Stanislav V.
full_name: Kremnyov, Stanislav V.
last_name: Kremnyov
citation:
ama: Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury
genes in Hydrozoa involves duplications, divergence, and neofunctionalization.
Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8
apa: Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P.,
Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury
genes in Hydrozoa involves duplications, divergence, and neofunctionalization.
Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8
chicago: Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva,
Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary
History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and
Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.
ieee: A. A. Vetrova et al., “The evolutionary history of Brachyury genes
in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific
Reports, vol. 13. Springer Nature, 2023.
ista: Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov
SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications,
divergence, and neofunctionalization. Scientific Reports. 13, 9382.
mla: Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes
in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific
Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8.
short: A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia,
S.V. Kremnyov, Scientific Reports 13 (2023).
date_created: 2023-06-25T22:00:46Z
date_published: 2023-06-09T00:00:00Z
date_updated: 2023-08-02T06:17:18Z
day: '09'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1038/s41598-023-35979-8
external_id:
isi:
- '001006690200045'
pmid:
- '37296138'
file:
- access_level: open_access
checksum: baddf6b2fa9adf88263d4a3b0998f0f2
content_type: application/pdf
creator: dernst
date_created: 2023-06-26T09:58:53Z
date_updated: 2023-06-26T09:58:53Z
file_id: '13170'
file_name: 2023_ScientificReports_Vetrova.pdf
file_size: 4844149
relation: main_file
success: 1
file_date_updated: 2023-06-26T09:58:53Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolutionary history of Brachyury genes in Hydrozoa involves duplications,
divergence, and neofunctionalization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '13138'
abstract:
- lang: eng
text: "We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed
away from integrability by an isotropic next-to-nearest neighbor exchange interaction.
Recently, it was conjectured that this model possesses an infinite tower of quasiconserved
integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)].
In this work we first test this conjecture by investigating how the norm of the
adiabatic gauge potential (AGP) scales with the system size, which is known to
be a remarkably accurate measure of chaos. We find that for the perturbed XXX
chain the behavior of the AGP norm corresponds to neither an integrable nor a
chaotic regime, which supports the conjectured quasi-integrability of the model.
We then prove the conjecture and explicitly construct the infinite set of quasiconserved
charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest
exchange interaction can be viewed as a truncation of an integrable long-range
deformation of the Heisenberg spin chain."
acknowledgement: "The numerical computations in this work were performed using QuSpin
[83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler,
Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant
and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively.
We are grateful to an anonymous referee for very useful comments and for drawing
our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium,
a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded
by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially
supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant
101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS)
- research programme P1-0402. "
article_number: '184312'
article_processing_charge: No
article_type: original
author:
- first_name: Pavel
full_name: Orlov, Pavel
last_name: Orlov
- first_name: Anastasiia
full_name: Tiutiakina, Anastasiia
last_name: Tiutiakina
- first_name: Rustem
full_name: Sharipov, Rustem
last_name: Sharipov
- first_name: Elena
full_name: Petrova, Elena
id: 0ac84990-897b-11ed-a09c-f5abb56a4ede
last_name: Petrova
- first_name: Vladimir
full_name: Gritsev, Vladimir
last_name: Gritsev
- first_name: Denis V.
full_name: Kurlov, Denis V.
last_name: Kurlov
citation:
ama: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic
eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical
Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312
apa: Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov,
D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking
of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312
chicago: Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir
Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability
Breaking of Heisenberg Chain.” Physical Review B. American Physical Society,
2023. https://doi.org/10.1103/PhysRevB.107.184312.
ieee: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov,
“Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg
chain,” Physical Review B, vol. 107, no. 18. American Physical Society,
2023.
ista: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023.
Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg
chain. Physical Review B. 107(18), 184312.
mla: Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability
Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312,
American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.
short: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov,
Physical Review B 107 (2023).
date_created: 2023-06-18T22:00:46Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-02T06:16:02Z
day: '01'
department:
- _id: GradSch
doi: 10.1103/PhysRevB.107.184312
external_id:
arxiv:
- '2303.00729'
isi:
- '001003686900004'
intvolume: ' 107'
isi: 1
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.00729
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg
chain
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '13213'
abstract:
- lang: eng
text: The primary cell wall is a fundamental plant constituent that is flexible
but sufficiently rigid to support the plant cell shape. Although many studies
have demonstrated that reactive oxygen species (ROS) serve as important signaling
messengers to modify the cell wall structure and affect cellular growth, the regulatory
mechanism underlying the spatial-temporal regulation of ROS activity for cell
wall maintenance remains largely unclear. Here, we demonstrate the role of the
Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5)
and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating
ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division
planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide
adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in
the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level
or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5
sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment,
and iron over-accumulated in the walls between the root epidermis and cortex cell
layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial
for membrane association and functionality of SKU5 and SKS1. Overall, our results
identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation
of cell wall structure and root cell growth.
acknowledgement: We thank Dong liu for offering iron staining technique; ZhiChang
Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang
and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for
a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke
Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan
Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia
Li for helping with sample preparation, and taking TEM images, at the Center for
Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.
article_processing_charge: No
article_type: original
author:
- first_name: C
full_name: Chen, C
last_name: Chen
- first_name: Y
full_name: Zhang, Y
last_name: Zhang
- first_name: J
full_name: Cai, J
last_name: Cai
- first_name: Y
full_name: Qiu, Y
last_name: Qiu
- first_name: L
full_name: Li, L
last_name: Li
- first_name: C
full_name: Gao, C
last_name: Gao
- first_name: Y
full_name: Gao, Y
last_name: Gao
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: S
full_name: Wu, S
last_name: Wu
- first_name: C
full_name: Wei, C
last_name: Wei
- first_name: J
full_name: Chen, J
last_name: Chen
- first_name: T
full_name: Xu, T
last_name: Xu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Wang, J
last_name: Wang
- first_name: R
full_name: Li, R
last_name: Li
- first_name: D
full_name: Chao, D
last_name: Chao
- first_name: B
full_name: Zhang, B
last_name: Zhang
- first_name: X
full_name: Chen, X
last_name: Chen
- first_name: Z
full_name: Gao, Z
last_name: Gao
citation:
ama: Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate
cell wall formation using apoplastic redox-based reactions in roots. Plant
Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207
apa: Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper
oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based
reactions in roots. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1093/plphys/kiad207
chicago: Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper
Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based
Reactions in Roots.” Plant Physiology. American Society of Plant Biologists,
2023. https://doi.org/10.1093/plphys/kiad207.
ieee: C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell
wall formation using apoplastic redox-based reactions in roots,” Plant Physiology,
vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.
ista: Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen
J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper
oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based
reactions in roots. Plant Physiology. 192(3), 2243–2260.
mla: Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall
Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology,
vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.
short: C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C.
Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z.
Gao, Plant Physiology 192 (2023) 2243–2260.
date_created: 2023-07-12T07:32:58Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:27:55Z
day: '01'
ddc:
- '575'
department:
- _id: JiFr
doi: 10.1093/plphys/kiad207
external_id:
isi:
- '000971795800001'
pmid:
- '37010107'
file:
- access_level: open_access
checksum: 5492e1d18ac3eaf202633d210fa0fb75
content_type: application/pdf
creator: cchlebak
date_created: 2023-07-13T13:26:33Z
date_updated: 2023-07-13T13:26:33Z
file_id: '13220'
file_name: 2023_PlantPhys_Chen.pdf
file_size: 2076977
relation: main_file
success: 1
file_date_updated: 2023-07-13T13:26:33Z
has_accepted_license: '1'
intvolume: ' 192'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2243-2260
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic
redox-based reactions in roots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 192
year: '2023'
...
---
_id: '12478'
abstract:
- lang: eng
text: In Gram negative bacteria, the multiple antibiotic resistance or mar operon,
is known to control the expression of multi-drug efflux genes that protect bacteria
from a wide range of drugs. As many different chemical compounds can induce this
operon, identifying the parameters that govern the dynamics of its induction is
crucial to better characterize the processes of tolerance and resistance. Most
experiments have assumed that the properties of the mar transcriptional network
can be inferred from population measurements. However, measurements from an asynchronous
population of cells can mask underlying phenotypic variations of single cells.
We monitored the activity of the mar promoter in single Escherichia coli cells
in linear micro-colonies and established that the response to a steady level of
inducer was most heterogeneous within individual colonies for an intermediate
value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells
exhibited similar promoter activity, whereas activity was greatly variable between
different sub-lineages. Specific sub-trees of uniform promoter activity persisted
over several generations. Statistical analyses of the lineages suggest that the
presence of these sub-trees is the signature of an inducible memory of the promoter
state that is transmitted from mother to daughter cells. This single-cell study
reveals that the degree of epigenetic inheritance changes as a function of inducer
concentration, suggesting that phenotypic inheritance may be an inducible phenotype.
acknowledgement: This work was supported by NIH P50 award P50GM081892-02 to the University
of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support
from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship
to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.
article_number: '1049255'
article_processing_charge: Yes
article_type: original
author:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: L
full_name: Bruneaux, L
last_name: Bruneaux
- first_name: P
full_name: Oikonomou, P
last_name: Oikonomou
- first_name: M
full_name: Aldana, M
last_name: Aldana
- first_name: P
full_name: Cluzel, P
last_name: Cluzel
citation:
ama: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of
growing and dividing bacteria reveals an inducible memory of mar operon
expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255
apa: Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023).
Monitoring lineages of growing and dividing bacteria reveals an inducible memory
of mar operon expression. Frontiers in Microbiology. Frontiers.
https://doi.org/10.3389/fmicb.2023.1049255
chicago: Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring
Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar
Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255.
ieee: C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring
lineages of growing and dividing bacteria reveals an inducible memory of mar
operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.
ista: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages
of growing and dividing bacteria reveals an inducible memory of mar operon
expression. Frontiers in Microbiology. 14, 1049255.
mla: Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria
Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in
Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255.
short: C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in
Microbiology 14 (2023).
date_created: 2023-02-02T08:13:28Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2023-08-02T06:25:04Z
day: '20'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.3389/fmicb.2023.1049255
external_id:
isi:
- '001030002600001'
pmid:
- '37485524'
file:
- access_level: open_access
checksum: 7dd322347512afaa5daf72a0154f2f07
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:16:34Z
date_updated: 2023-07-31T07:16:34Z
file_id: '13322'
file_name: 2023_FrontiersMicrobiology_Guet.pdf
file_size: 6452841
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:16:34Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring lineages of growing and dividing bacteria reveals an inducible memory
of mar operon expression
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13229'
abstract:
- lang: eng
text: Dynamic reorganization of the cytoplasm is key to many core cellular processes,
such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements
are thought to constitute the main drivers of cytoplasmic flows and reorganization.
In contrast, remarkably little is known about how dynamic changes in size and
shape of cell organelles affect cytoplasmic organization. Here, we show that within
the maturing zebrafish oocyte, the surface localization of exocytosis-competent
cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by
the combined activities of yolk granule (Yg) fusion and microtubule aster formation
and translocation. We find that Cgs are moved towards the oocyte surface through
radially outward cytoplasmic flows induced by Ygs fusing and compacting towards
the oocyte center in response to GVBD. We further show that vesicles decorated
with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and
exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation
is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule
asters, the formation of which is induced by the release of CyclinB/Cdk1 upon
GVBD, and which display a net movement towards the oocyte surface by preferentially
binding to the oocyte actin cortex. We finally demonstrate that the decoration
of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent
chorion elevation, a process central in egg activation. Collectively, these findings
unravel a yet unrecognized role of organelle fusion, functioning together with
cytoskeletal rearrangements, in orchestrating cytoplasmic organization during
oocyte maturation.
acknowledgement: This work was supported by funding from the European Union (European
Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study
design, data collection and analysis, decision to publish, or preparation of the
manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Laura
full_name: Hofmann, Laura
id: b88d43f2-dc74-11ea-a0a7-e41b7912e031
last_name: Hofmann
- first_name: Irene
full_name: Steccari, Irene
id: 2705C766-9FE2-11EA-B224-C6773DDC885E
last_name: Steccari
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule
fusion and microtubule aster formation regulate cortical granule translocation
and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146.
doi:10.1371/journal.pbio.3002146
apa: Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P.
J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical
granule translocation and exocytosis in zebrafish oocytes. PLoS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146
chicago: Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp
J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical
Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146.
ieee: S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg,
“Yolk granule fusion and microtubule aster formation regulate cortical granule
translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol.
21, no. 6. Public Library of Science, p. e3002146, 2023.
ista: Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk
granule fusion and microtubule aster formation regulate cortical granule translocation
and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.
mla: Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation
Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.”
PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146,
doi:10.1371/journal.pbio.3002146.
short: S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS
Biology 21 (2023) e3002146.
date_created: 2023-07-16T22:01:09Z
date_published: 2023-06-08T00:00:00Z
date_updated: 2023-08-02T06:33:14Z
day: '08'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.3002146
ec_funded: 1
external_id:
isi:
- '001003199100005'
pmid:
- '37289834'
file:
- access_level: open_access
checksum: 8e88cb0e5a6433a2f1939a9030bed384
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:59:58Z
date_updated: 2023-07-18T07:59:58Z
file_id: '13246'
file_name: 2023_PloSBiology_Shamipour.pdf
file_size: 4431723
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:59:58Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: e3002146
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Yolk granule fusion and microtubule aster formation regulate cortical granule
translocation and exocytosis in zebrafish oocytes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2023'
...
---
_id: '13197'
abstract:
- lang: eng
text: "Nominally identical materials exchange net electric charge during contact
through a mechanism that is still debated. ‘Mosaic models’, in which surfaces
are presumed to consist of a random patchwork of microscopic donor/acceptor sites,
offer an appealing explanation for this phenomenon. However, recent experiments
have shown that global differences persist even between same-material samples,
which the standard mosaic framework does not account for. Here, we expand the
mosaic framework by incorporating global differences in the densities of donor/acceptor
sites. We develop\r\nan analytical model, backed by numerical simulations, that
smoothly connects the global and deterministic charge transfer of different materials
to the local and stochastic mosaic picture normally associated with identical
materials. Going further, we extend our model to explain the effect of contact
asymmetries during sliding, providing a plausible explanation for reversal of
charging sign that has been observed experimentally."
acknowledgement: "This project has received funding from the European Research Council
Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. "
article_number: '065601'
article_processing_charge: No
article_type: original
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing
mosaic models to different-material samples and sliding contacts. Physical
Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601'
apa: 'Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric
charging: Generalizing mosaic models to different-material samples and sliding
contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601'
chicago: 'Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric
Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding
Contacts.” Physical Review Materials. American Physical Society, 2023.
https://doi.org/10.1103/physrevmaterials.7.065601.'
ieee: 'G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging:
Generalizing mosaic models to different-material samples and sliding contacts,”
Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.'
ista: 'Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging:
Generalizing mosaic models to different-material samples and sliding contacts.
Physical Review Materials. 7(6), 065601.'
mla: 'Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric
Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding
Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical
Society, 2023, doi:10.1103/physrevmaterials.7.065601.'
short: G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).
date_created: 2023-07-07T12:48:01Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2023-08-02T06:34:47Z
day: '13'
ddc:
- '537'
department:
- _id: ScWa
doi: 10.1103/physrevmaterials.7.065601
ec_funded: 1
external_id:
arxiv:
- '2304.12861'
isi:
- '001019565900002'
file:
- access_level: open_access
checksum: 75584730d9cdd50eeccb4c52c509776d
content_type: application/pdf
creator: ggrosjea
date_created: 2023-07-07T12:49:51Z
date_updated: 2023-07-07T12:49:51Z
file_id: '13198'
file_name: Mosaic_asymmetries.pdf
file_size: 1127040
relation: main_file
success: 1
file_date_updated: 2023-07-07T12:49:51Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '6'
keyword:
- Physics and Astronomy (miscellaneous)
- General Materials Science
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Materials
publication_identifier:
issn:
- 2475-9953
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Asymmetries in triboelectric charging: Generalizing mosaic models to different-material
samples and sliding contacts'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2023'
...
---
_id: '13230'
abstract:
- lang: eng
text: 'To interpret the sensory environment, the brain combines ambiguous sensory
measurements with knowledge that reflects context-specific prior experience. But
environmental contexts can change abruptly and unpredictably, resulting in uncertainty
about the current context. Here we address two questions: how should context-specific
prior knowledge optimally guide the interpretation of sensory stimuli in changing
environments, and do human decision-making strategies resemble this optimum? We
probe these questions with a task in which subjects report the orientation of
ambiguous visual stimuli that were drawn from three dynamically switching distributions,
representing different environmental contexts. We derive predictions for an ideal
Bayesian observer that leverages knowledge about the statistical structure of
the task to maximize decision accuracy, including knowledge about the dynamics
of the environment. We show that its decisions are biased by the dynamically changing
task context. The magnitude of this decision bias depends on the observer’s continually
evolving belief about the current context. The model therefore not only predicts
that decision bias will grow as the context is indicated more reliably, but also
as the stability of the environment increases, and as the number of trials since
the last context switch grows. Analysis of human choice data validates all three
predictions, suggesting that the brain leverages knowledge of the statistical
structure of environmental change when interpreting ambiguous sensory signals.'
acknowledgement: The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable
discussion and feedback.
article_number: e1011104
article_processing_charge: No
article_type: original
author:
- first_name: Julie A.
full_name: Charlton, Julie A.
last_name: Charlton
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Yoon H.
full_name: Bai, Yoon H.
last_name: Bai
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
- first_name: Robbe L.T.
full_name: Goris, Robbe L.T.
last_name: Goris
citation:
ama: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental
dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6).
doi:10.1371/journal.pcbi.1011104
apa: Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris,
R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104
chicago: Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad,
and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.”
PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.
ieee: J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T.
Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational
Biology, vol. 19, no. 6. Public Library of Science, 2023.
ista: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental
dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.
mla: Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision
Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library
of Science, 2023, doi:10.1371/journal.pcbi.1011104.
short: J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris,
PLoS Computational Biology 19 (2023).
date_created: 2023-07-16T22:01:09Z
date_published: 2023-06-08T00:00:00Z
date_updated: 2023-08-02T06:33:50Z
day: '08'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1371/journal.pcbi.1011104
external_id:
isi:
- '001003410200003'
pmid:
- '37289753'
file:
- access_level: open_access
checksum: 800761fa2c647fabd6ad034589bc526e
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T08:07:59Z
date_updated: 2023-07-18T08:07:59Z
file_id: '13247'
file_name: 2023_PloSCompBio_Charlton.pdf
file_size: 2281868
relation: main_file
success: 1
file_date_updated: 2023-07-18T08:07:59Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Environmental dynamics shape perceptual decision bias
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '13232'
abstract:
- lang: eng
text: The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus
has led to its rapid spread, causing over 600 million confirmed cases and more
than 6.5 million confirmed deaths. The huge demand for the rapid development and
deployment of low-cost and effective vaccines against emerging variants has renewed
interest in DNA vaccine technology. Here, we report the rapid generation and immunological
evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron
variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP).
The delivery of DNA vaccines using electroporation in a two-dose regimen induced
high-antibody titers and profound cellular responses in mice. The antibody titers
induced against the Omicron variant of the vaccine were sufficient for effective
protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein
in the vaccine construct shifted the immune response to the favorable Th1-like
type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery
by needle-free injection allowed us to achieve antibody titers comparable with
mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform
as a promising solution for robust and effective SARS-CoV-2 protection, supporting
further translational study.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article, or the decision to submit it for publication.
The authors express their gratitude to the Institute of Physiology of the National
Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.
article_number: '1014'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Maria
full_name: Stegantseva, Maria
last_name: Stegantseva
- first_name: Sergey
full_name: Golenchenko, Sergey
last_name: Golenchenko
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Dzmitry
full_name: Lutskovich, Dzmitry
last_name: Lutskovich
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
citation:
ama: Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of
SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6).
doi:10.3390/vaccines11061014
apa: Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M.,
Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014
chicago: Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko,
Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander
Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP
Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.
ieee: D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI,
2023.
ista: Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S,
Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2
DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.
mla: Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine
Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI,
2023, doi:10.3390/vaccines11061014.
short: D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S.
Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-02T06:31:19Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/vaccines11061014
external_id:
isi:
- '001017740000001'
file:
- access_level: open_access
checksum: 8f484c0f30f8699c589b1c29a0fd7d7f
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:25:43Z
date_updated: 2023-07-18T07:25:43Z
file_id: '13244'
file_name: 2023_Vaccines_Dormeshkin.pdf
file_size: 2339746
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:25:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Vaccines
publication_identifier:
eissn:
- 2076-393X
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion
protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2023'
...
---
_id: '13231'
abstract:
- lang: eng
text: We study ab initio approaches for calculating x-ray Thomson scattering spectra
from density functional theory molecular dynamics simulations based on a modified
Chihara formula that expresses the inelastic contribution in terms of the dielectric
function. We study the electronic dynamic structure factor computed from the Mermin
dielectric function using an ab initio electron-ion collision frequency in comparison
to computations using a linear-response time-dependent density functional theory
(LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion
of free-free and bound-free contributions to the scattering signal. A separate
treatment of these contributions, where only the free-free part follows the Mermin
dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium,
but breaks down for highly compressed matter where the bound states become pressure
ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on
beryllium demonstrating strong deviations from the plasma conditions inferred
with traditional analytic models at small scattering angles.
acknowledgement: "We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H.
J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support
by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440.
All simulations and analyses were performed at the North-German Supercomputing Alliance
(HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges
support by the European Horizon 2020 programme within the Marie Sklodowska-Curie
actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed
under the auspices of the U.S. Department of Energy by Lawrence Livermore National
Laboratory under Contract No. DE-AC52-07NA27344."
article_number: '065207'
article_processing_charge: No
article_type: original
author:
- first_name: Maximilian
full_name: Schörner, Maximilian
last_name: Schörner
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: Tilo
full_name: Döppner, Tilo
last_name: Döppner
- first_name: Dominik
full_name: Kraus, Dominik
last_name: Kraus
- first_name: Luke B.
full_name: Fletcher, Luke B.
last_name: Fletcher
- first_name: Siegfried H.
full_name: Glenzer, Siegfried H.
last_name: Glenzer
- first_name: Ronald
full_name: Redmer, Ronald
last_name: Redmer
citation:
ama: Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra
from density functional theory molecular dynamics simulations based on a modified
Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207
apa: Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer,
S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density
functional theory molecular dynamics simulations based on a modified Chihara formula.
Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207
chicago: Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus,
Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering
Spectra from Density Functional Theory Molecular Dynamics Simulations Based on
a Modified Chihara Formula.” Physical Review E. American Physical Society,
2023. https://doi.org/10.1103/PhysRevE.107.065207.
ieee: M. Schörner et al., “X-ray Thomson scattering spectra from density
functional theory molecular dynamics simulations based on a modified Chihara formula,”
Physical Review E, vol. 107, no. 6. American Physical Society, 2023.
ista: Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer
R. 2023. X-ray Thomson scattering spectra from density functional theory molecular
dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6),
065207.
mla: Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density
Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.”
Physical Review E, vol. 107, no. 6, 065207, American Physical Society,
2023, doi:10.1103/PhysRevE.107.065207.
short: M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer,
R. Redmer, Physical Review E 107 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-08-02T06:30:46Z
day: '14'
department:
- _id: BiCh
doi: 10.1103/PhysRevE.107.065207
external_id:
arxiv:
- '2301.01545'
isi:
- '001020265000002'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.01545
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: X-ray Thomson scattering spectra from density functional theory molecular dynamics
simulations based on a modified Chihara formula
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '13233'
abstract:
- lang: eng
text: We study the impact of finite-range physics on the zero-range-model analysis
of three-body recombination in ultracold atoms. We find that temperature dependence
of the zero-range parameters can vary from one set of measurements to another
as it may be driven by the distribution of error bars in the experiment, and not
by the underlying three-body physics. To study finite-temperature effects in three-body
recombination beyond the zero-range physics, we introduce and examine a finite-range
model based upon a hyperspherical formalism. The systematic error discussed in
this Letter may provide a significant contribution to the error bars of measured
three-body parameters.
acknowledgement: We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful
discussions. M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON).
article_number: L061304
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sofya
full_name: Agafonova, Sofya
id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80
last_name: Agafonova
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body
loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304
apa: Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias
in fitting three-body loss to the zero-range model. Physical Review A.
American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304
chicago: Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range
Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.
ieee: S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting
three-body loss to the zero-range model,” Physical Review A, vol. 107,
no. 6. American Physical Society, 2023.
ista: Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body
loss to the zero-range model. Physical Review A. 107(6), L061304.
mla: Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the
Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American
Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.
short: S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2023-08-02T06:31:52Z
day: '20'
department:
- _id: MiLe
- _id: OnHo
doi: 10.1103/PhysRevA.107.L061304
ec_funded: 1
external_id:
arxiv:
- '2302.01022'
isi:
- '001019748000005'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.01022
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finite-range bias in fitting three-body loss to the zero-range model
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '13256'
abstract:
- lang: eng
text: The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM,
or monsoon) are two giants of tropical climate. Here we assess the future evolution
of the ENSO-monsoon teleconnection in climate simulations with idealized forcing
of CO2 increment at a rate of 1% year-1 starting from a present-day condition
(367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon
teleconnection with the increase in CO2. Increased co-occurrences of El Niño and
positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection.
Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature
(SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and
an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of
the strength of the Indian monsoon, a weakening of this relation may mean a less
predictable Indian monsoon in a warmer climate.
acknowledgement: This work was supported by National Research Foundation of Korea
(NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000).
Model simulation and data transfer were supported by the National Supercomputing
Center with supercomputing resources including technical support (KSC-2019-CHA-0005),
the National Center for Meteorological Supercomputer of the Korea Meteorological
Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET),
respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science
and Technology, Pohang, South Korea for the model simulations.
article_number: '82'
article_processing_charge: Yes
article_type: original
author:
- first_name: Bidyut B
full_name: Goswami, Bidyut B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: Goswami
- first_name: Soon Il
full_name: An, Soon Il
last_name: An
citation:
ama: GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming
climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5
apa: GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection
in a warming climate. Npj Climate and Atmospheric Science. Springer Nature.
https://doi.org/10.1038/s41612-023-00411-5
chicago: GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature,
2023. https://doi.org/10.1038/s41612-023-00411-5.
ieee: B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection
in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer
Nature, 2023.
ista: GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection
in a warming climate. npj Climate and Atmospheric Science. 6, 82.
mla: GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82,
Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.
short: B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-08T00:00:00Z
date_updated: 2023-08-02T06:38:07Z
day: '08'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1038/s41612-023-00411-5
external_id:
isi:
- '001024920300002'
file:
- access_level: open_access
checksum: e9967d436a83b8ffcc6f58782e1f7500
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:00:01Z
date_updated: 2023-07-31T08:00:01Z
file_id: '13326'
file_name: 2023_npjclimate_Goswami.pdf
file_size: 1750712
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:00:01Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: npj Climate and Atmospheric Science
publication_identifier:
eissn:
- 2397-3722
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An assessment of the ENSO-monsoon teleconnection in a warming climate
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2023'
...
---
_id: '13260'
abstract:
- lang: eng
text: Experimental evolution studies are powerful approaches to examine the evolutionary
history of lab populations. Such studies have shed light on how selection changes
phenotypes and genotypes. Most of these studies have not examined the time course
of adaptation under sexual selection manipulation, by resequencing the populations’
genomes at multiple time points. Here, we analyze allele frequency trajectories
in Drosophila pseudoobscura where we altered their sexual selection regime for
200 generations and sequenced pooled populations at 5 time points. The intensity
of sexual selection was either relaxed in monogamous populations (M) or elevated
in polyandrous lines (E). We present a comprehensive study of how selection alters
population genetics parameters at the chromosome and gene level. We investigate
differences in the effective population size—Ne—between the treatments, and perform
a genome-wide scan to identify signatures of selection from the time-series data.
We found genomic signatures of adaptation to both regimes in D. pseudoobscura.
There are more significant variants in E lines as expected from stronger sexual
selection. However, we found that the response on the X chromosome was substantial
in both treatments, more pronounced in E and restricted to the more recently sex-linked
chromosome arm XR in M. In the first generations of experimental evolution, we
estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive
response at the onset of selection. Additionally, the third chromosome was affected
by elevated polyandry whereby its distal end harbors a region showing a strong
signal of adaptive evolution especially in E lines.
acknowledgement: This work was supported by the Vienna Science and Technology Fund
(WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315)
and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC
(UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed
on the computer cluster at the University of St Andrews Bioinformatics Unit, which
is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing
was carried out with the computational resources provided by the Research/Scientific
Computing teams at The James Hutton Institute and the National Institute of Agricultural
Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1.
We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about
the project as well as providing us with the resequencing data they had produced
as a result of previous work on this experiment. We are especially grateful to Tanya
Sneddon for her help with the DNA extraction process and shipping.
article_number: evad113
article_processing_charge: Yes
article_type: original
author:
- first_name: Carolina
full_name: De Castro Barbosa Rodrigues Barata, Carolina
id: 20565186-803f-11ed-ab7e-96a4ff7694ef
last_name: De Castro Barbosa Rodrigues Barata
- first_name: Rhonda R.
full_name: Snook, Rhonda R.
last_name: Snook
- first_name: Michael G.
full_name: Ritchie, Michael G.
last_name: Ritchie
- first_name: Carolin
full_name: Kosiol, Carolin
last_name: Kosiol
citation:
ama: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection
on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila
pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113'
apa: 'de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &
Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual
selection regime in Drosophila pseudoobscura. Genome Biology and Evolution.
Oxford Academic. https://doi.org/10.1093/gbe/evad113'
chicago: 'Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael
G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to
an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology
and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.'
ieee: 'C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C.
Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection
regime in Drosophila pseudoobscura,” Genome biology and evolution, vol.
15, no. 7. Oxford Academic, 2023.'
ista: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023.
Selection on the fly: Short-term adaptation to an altered sexual selection regime
in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.'
mla: 'de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly:
Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.”
Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic,
2023, doi:10.1093/gbe/evad113.'
short: C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol,
Genome Biology and Evolution 15 (2023).
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:42:35Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evad113
external_id:
isi:
- '001023444700003'
pmid:
- '37341535'
file:
- access_level: open_access
checksum: 70de3c4878de6efe00dc56de2df8812f
content_type: application/pdf
creator: dernst
date_created: 2023-08-01T06:58:34Z
date_updated: 2023-08-01T06:58:34Z
file_id: '13339'
file_name: 2023_GBE_Barata.pdf
file_size: 2382587
relation: main_file
success: 1
file_date_updated: 2023-08-01T06:58:34Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/carolbarata/dpseudo-n-beyond
scopus_import: '1'
status: public
title: 'Selection on the fly: Short-term adaptation to an altered sexual selection
regime in Drosophila pseudoobscura'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2023'
...
---
_id: '13346'
abstract:
- lang: eng
text: The self-assembly of nanoparticles driven by small molecules or ions may produce
colloidal superlattices with features and properties reminiscent of those of metals
or semiconductors. However, to what extent the properties of such supramolecular
crystals actually resemble those of atomic materials often remains unclear. Here,
we present coarse-grained molecular simulations explicitly demonstrating how a
behavior evocative of that of semiconductors may emerge in a colloidal superlattice.
As a case study, we focus on gold nanoparticles bearing positively charged groups
that self-assemble into FCC crystals via mediation by citrate counterions. In
silico ohmic experiments show how the dynamically diverse behavior of the ions
in different superlattice domains allows the opening of conductive ionic gates
above certain levels of applied electric fields. The observed binary conductive/nonconductive
behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular
level, crossing the “band gap” requires a sufficient electrostatic stimulus to
break the intermolecular interactions and make ions diffuse throughout the superlattice’s
cavities.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Lionello, Chiara
last_name: Lionello
- first_name: Claudio
full_name: Perego, Claudio
last_name: Perego
- first_name: Andrea
full_name: Gardin, Andrea
last_name: Gardin
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Giovanni M.
full_name: Pavan, Giovanni M.
last_name: Pavan
citation:
ama: Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. Supramolecular semiconductivity
through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano.
2023;17(1):275-287. doi:10.1021/acsnano.2c07558
apa: Lionello, C., Perego, C., Gardin, A., Klajn, R., & Pavan, G. M. (2023).
Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle
superlattices. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.2c07558
chicago: Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni
M. Pavan. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle
Superlattices.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.2c07558.
ieee: C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. M. Pavan, “Supramolecular
semiconductivity through emerging ionic gates in ion–nanoparticle superlattices,”
ACS Nano, vol. 17, no. 1. American Chemical Society, pp. 275–287, 2023.
ista: Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. 2023. Supramolecular semiconductivity
through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 17(1),
275–287.
mla: Lionello, Chiara, et al. “Supramolecular Semiconductivity through Emerging
Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano, vol. 17, no.
1, American Chemical Society, 2023, pp. 275–87, doi:10.1021/acsnano.2c07558.
short: C. Lionello, C. Perego, A. Gardin, R. Klajn, G.M. Pavan, ACS Nano 17 (2023)
275–287.
date_created: 2023-08-01T09:30:29Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-02T06:51:15Z
day: '10'
doi: 10.1021/acsnano.2c07558
extern: '1'
intvolume: ' 17'
issue: '1'
keyword:
- General Physics and Astronomy
- General Engineering
- General Materials Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.2c07558
month: '01'
oa: 1
oa_version: Published Version
page: 275-287
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle
superlattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2023'
...
---
_id: '13447'
abstract:
- lang: eng
text: Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology
is a prime example, with oscillation periods and amplitudes that are readily detectable
with time-domain space-based telescopes. These oscillations can be used to infer
masses, ages and radii for large numbers of stars, providing unique constraints
on stellar populations in our galaxy. The cadence, duration, and spatial resolution
of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology
and will probe an important population not studied by prior missions. We identify
photometric precision as a key requirement for realizing the potential of asteroseismology
with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars
will enable detections of the populous red clump star population in the Galactic
bulge. If the survey efficiency is better than expected, we argue for repeat observations
of the same fields to improve photometric precision, or covering additional fields
to expand the stellar population reach if the photometric precision for saturated
stars is better than 1 mmag. Asteroseismology is relatively insensitive to the
timing of the observations during the mission, and the prime red clump targets
can be observed in a single 70 day campaign in any given field. Complementary
stellar characterization, particularly astrometry tied to the Gaia system, will
also dramatically expand the diagnostic power of asteroseismology. We also highlight
synergies to Roman GBTDS exoplanet science using transits and microlensing.
article_number: '2307.03237'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Huber, Daniel
last_name: Huber
- first_name: Marc
full_name: Pinsonneault, Marc
last_name: Pinsonneault
- first_name: Paul
full_name: Beck, Paul
last_name: Beck
- first_name: Timothy R.
full_name: Bedding, Timothy R.
last_name: Bedding
- first_name: Joss Bland-Hawthorn
full_name: Joss Bland-Hawthorn, Joss Bland-Hawthorn
last_name: Joss Bland-Hawthorn
- first_name: Sylvain N.
full_name: Breton, Sylvain N.
last_name: Breton
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: William J.
full_name: Chaplin, William J.
last_name: Chaplin
- first_name: Rafael A.
full_name: Garcia, Rafael A.
last_name: Garcia
- first_name: Samuel K.
full_name: Grunblatt, Samuel K.
last_name: Grunblatt
- first_name: Joyce A.
full_name: Guzik, Joyce A.
last_name: Guzik
- first_name: Saskia
full_name: Hekker, Saskia
last_name: Hekker
- first_name: Steven D.
full_name: Kawaler, Steven D.
last_name: Kawaler
- first_name: Stephane
full_name: Mathis, Stephane
last_name: Mathis
- first_name: Savita
full_name: Mathur, Savita
last_name: Mathur
- first_name: Travis
full_name: Metcalfe, Travis
last_name: Metcalfe
- first_name: Benoit
full_name: Mosser, Benoit
last_name: Mosser
- first_name: Melissa K.
full_name: Ness, Melissa K.
last_name: Ness
- first_name: Anthony L.
full_name: Piro, Anthony L.
last_name: Piro
- first_name: Aldo
full_name: Serenelli, Aldo
last_name: Serenelli
- first_name: Sanjib
full_name: Sharma, Sanjib
last_name: Sharma
- first_name: David R.
full_name: Soderblom, David R.
last_name: Soderblom
- first_name: Keivan G.
full_name: Stassun, Keivan G.
last_name: Stassun
- first_name: Dennis
full_name: Stello, Dennis
last_name: Stello
- first_name: Jamie
full_name: Tayar, Jamie
last_name: Tayar
- first_name: Gerard T. van
full_name: Belle, Gerard T. van
last_name: Belle
- first_name: Joel C.
full_name: Zinn, Joel C.
last_name: Zinn
citation:
ama: Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic
bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237
apa: Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn,
J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman
galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237
chicago: Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn
Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology
with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.
ieee: D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain
survey,” arXiv. .
ista: Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton
SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler
SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma
S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology
with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.
mla: Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain
Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.
short: D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn,
S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik,
S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness,
A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J.
Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).
date_created: 2023-08-02T07:30:43Z
date_published: 2023-07-06T00:00:00Z
date_updated: 2023-08-02T07:36:00Z
day: '06'
department:
- _id: LiBu
doi: 10.48550/arXiv.2307.03237
external_id:
arxiv:
- '2307.03237'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.03237
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Asteroseismology with the Roman galactic bulge time-domain survey
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13354'
abstract:
- lang: eng
text: 'Integrating light-sensitive molecules within nanoparticle (NP) assemblies
is an attractive approach to fabricate new photoresponsive nanomaterials. Here,
we describe the concept of photocleavable anionic glue (PAG): small trianions
capable of mediating interactions between (and inducing the aggregation of) cationic
NPs by means of electrostatic interactions. Exposure to light converts PAGs into
dianionic products incapable of maintaining the NPs in an assembled state, resulting
in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept,
we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety
and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which
absorbs light across the entire visible spectrum. Both PAGs were used to prepare
either amorphous NP assemblies or regular superlattices with a long-range NP order.
These NP aggregates disassembled rapidly upon light exposure for a specific time,
which could be tuned by the incident light wavelength or the amount of PAG used.
Selective excitation of the inorganic PAG in a system combining the two PAGs results
in a photodecomposition product that deactivates the organic PAG, enabling nontrivial
disassembly profiles under a single type of external stimulus.'
article_processing_charge: No
article_type: original
author:
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Tzuf Shay
full_name: Peled, Tzuf Shay
last_name: Peled
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive
nanoparticle aggregates. Journal of the American Chemical Society. 2023;145(7):4098-4108.
doi:10.1021/jacs.2c11973
apa: Wang, J., Peled, T. S., & Klajn, R. (2023). Photocleavable anionic glues
for light-responsive nanoparticle aggregates. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/jacs.2c11973
chicago: Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic
Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American
Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.2c11973.
ieee: J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive
nanoparticle aggregates,” Journal of the American Chemical Society, vol.
145, no. 7. American Chemical Society, pp. 4098–4108, 2023.
ista: Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive
nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108.
mla: Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle
Aggregates.” Journal of the American Chemical Society, vol. 145, no. 7,
American Chemical Society, 2023, pp. 4098–108, doi:10.1021/jacs.2c11973.
short: J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145
(2023) 4098–4108.
date_created: 2023-08-01T09:33:08Z
date_published: 2023-02-09T00:00:00Z
date_updated: 2023-08-02T10:44:22Z
day: '09'
doi: 10.1021/jacs.2c11973
extern: '1'
external_id:
pmid:
- '36757850'
intvolume: ' 145'
issue: '7'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/jacs.2c11973
month: '02'
oa: 1
oa_version: Published Version
page: 4098-4108
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Photocleavable anionic glues for light-responsive nanoparticle aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 145
year: '2023'
...
---
_id: '13074'
abstract:
- lang: eng
text: "Deep learning has become an integral part of a large number of important
applications, and many of the recent breakthroughs have been enabled by the ability
to train very large models, capable to capture complex patterns and relationships
from the data. At the same time, the massive sizes of modern deep learning models
have made their deployment to smaller devices more challenging; this is particularly
important, as in many applications the users rely on accurate deep learning predictions,
but they only have access to devices with limited memory and compute power. One
solution to this problem is to prune neural networks, by setting as many of their
parameters as possible to zero, to obtain accurate sparse models with lower memory
footprint. Despite the great research progress in obtaining sparse models that
preserve accuracy, while satisfying memory and computational constraints, there
are still many challenges associated with efficiently training sparse models,
as well as understanding their generalization properties.\r\n\r\nThe focus of
this thesis is to investigate how the training process of sparse models can be
made more efficient, and to understand the differences between sparse and dense
models in terms of how well they can generalize to changes in the data distribution.
We first study a method for co-training sparse and dense models, at a lower cost
compared to regular training. With our method we can obtain very accurate sparse
networks, and dense models that can recover the baseline accuracy. Furthermore,
we are able to more easily analyze the differences, at prediction level, between
the sparse-dense model pairs. Next, we investigate the generalization properties
of sparse neural networks in more detail, by studying how well different sparse
models trained on a larger task can adapt to smaller, more specialized tasks,
in a transfer learning scenario. Our analysis across multiple pruning methods
and sparsity levels reveals that sparse models provide features that can transfer
similarly to or better than the dense baseline. However, the choice of the pruning
method plays an important role, and can influence the results when the features
are fixed (linear finetuning), or when they are allowed to adapt to the new task
(full finetuning). Using sparse models with fixed masks for finetuning on new
tasks has an important practical advantage, as it enables training neural networks
on smaller devices. However, one drawback of current pruning methods is that the
entire training cycle has to be repeated to obtain the initial sparse model, for
every sparsity target; in consequence, the entire training process is costly and
also multiple models need to be stored. In the last part of the thesis we propose
a method that can train accurate dense models that are compressible in a single
step, to multiple sparsity levels, without additional finetuning. Our method results
in sparse models that can be competitive with existing pruning methods, and which
can also successfully generalize to new tasks."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
citation:
ama: Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074
apa: Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074
chicago: Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural
Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.
ieee: E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute
of Science and Technology Austria, 2023.
ista: Peste E-A. 2023. Efficiency and generalization of sparse neural networks.
Institute of Science and Technology Austria.
mla: Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.
short: E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute
of Science and Technology Austria, 2023.
date_created: 2023-05-23T17:07:53Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2023-08-04T10:33:27Z
day: '23'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
- _id: ChLa
doi: 10.15479/at:ista:13074
ec_funded: 1
file:
- access_level: open_access
checksum: 6b3354968403cb9d48cc5a83611fb571
content_type: application/pdf
creator: epeste
date_created: 2023-05-24T16:11:16Z
date_updated: 2023-05-24T16:11:16Z
file_id: '13087'
file_name: PhD_Thesis_Alexandra_Peste_final.pdf
file_size: 2152072
relation: main_file
success: 1
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checksum: 8d0df94bbcf4db72c991f22503b3fd60
content_type: application/zip
creator: epeste
date_created: 2023-05-24T16:12:59Z
date_updated: 2023-05-24T16:12:59Z
file_id: '13088'
file_name: PhD_Thesis_APeste.zip
file_size: 1658293
relation: source_file
file_date_updated: 2023-05-24T16:12:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '147'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11458'
relation: part_of_dissertation
status: public
- id: '13053'
relation: part_of_dissertation
status: public
- id: '12299'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: Efficiency and generalization of sparse neural networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13963'
abstract:
- lang: eng
text: The many-body localization (MBL) proximity effect is an intriguing phenomenon
where a thermal bath localizes due to the interaction with a disordered system.
The interplay of thermal and nonergodic behavior in these systems gives rise to
a rich phase diagram, whose exploration is an active field of research. In this
paper, we study a bosonic Hubbard model featuring two particle species representing
the bath and the disordered system. Using state-of-the-art numerical techniques,
we investigate the dynamics of the model in different regimes, based on which
we obtain a tentative phase diagram as a function of coupling strength and bath
size. When the bath is composed of a single particle, we observe clear signatures
of a transition from an MBL proximity effect to a delocalized phase. Increasing
the bath size, however, its thermalizing effect becomes stronger and eventually
the whole system delocalizes in the range of moderate interaction strengths studied.
In this regime, we characterize particle transport, revealing diffusive behavior
of the originally localized bosons.
acknowledgement: "We thank A. A. Michailidis and A. Mirlin for insightful discussions.
P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge
PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD
simulations were performed. The TEBD simulations were performed using the ITensor
library [60]."
article_number: '054201'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity
effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5).
doi:10.1103/physrevb.108.054201
apa: Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body
localization proximity effect in a two-species bosonic Hubbard model. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201
chicago: Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body
Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.
ieee: P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization
proximity effect in a two-species bosonic Hubbard model,” Physical Review B,
vol. 108, no. 5. American Physical Society, 2023.
ista: Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity
effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201.
mla: Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species
Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American
Physical Society, 2023, doi:10.1103/physrevb.108.054201.
short: P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).
date_created: 2023-08-05T18:25:22Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-08-07T09:51:39Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevb.108.054201
ec_funded: 1
external_id:
arxiv:
- '2303.16876'
file:
- access_level: open_access
checksum: f763000339b5fd543c14377109920690
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T09:48:08Z
date_updated: 2023-08-07T09:48:08Z
file_id: '13981'
file_name: 2023_PhysRevB_Brighi.pdf
file_size: 3051398
relation: main_file
success: 1
file_date_updated: 2023-08-07T09:48:08Z
has_accepted_license: '1'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Many-body localization proximity effect in a two-species bosonic Hubbard model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13966'
abstract:
- lang: eng
text: We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation
energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams,
we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation
energies up to n=5, with quadratic scaling in the number of basis functions. Our
technique reduces the computational complexity of the molecular many-fermion correlation
problem, opening up the possibility of low-scaling, accurate stochastic computations
for a wide class of many-body systems described by Hugenholtz diagrams.
acknowledgement: We acknowledge stimulating discussions with Sergey Varganov, Artur
Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov,
Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from
the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L.
acknowledges support by the FWF under Project No. P29902-N27, and by the European
Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported
by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research
Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg
STRUCTURES Excellence Cluster). The authors acknowledge support by the state of
Baden-Württemberg through bwHPC.
article_number: '045115'
article_processing_charge: No
article_type: original
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: T. V.
full_name: Tscherbul, T. V.
last_name: Tscherbul
citation:
ama: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic
correlation in molecules: High-order many-body perturbation theory with low scaling.
Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115'
apa: 'Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic
Monte Carlo for electronic correlation in molecules: High-order many-body perturbation
theory with low scaling. Physical Review B. American Physical Society.
https://doi.org/10.1103/PhysRevB.108.045115'
chicago: 'Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic
Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation
Theory with Low Scaling.” Physical Review B. American Physical Society,
2023. https://doi.org/10.1103/PhysRevB.108.045115.'
ieee: 'G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte
Carlo for electronic correlation in molecules: High-order many-body perturbation
theory with low scaling,” Physical Review B, vol. 108, no. 4. American
Physical Society, 2023.'
ista: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo
for electronic correlation in molecules: High-order many-body perturbation theory
with low scaling. Physical Review B. 108(4), 045115.'
mla: 'Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation
in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical
Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.'
short: G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).
date_created: 2023-08-06T22:01:10Z
date_published: 2023-07-15T00:00:00Z
date_updated: 2023-08-07T08:41:29Z
day: '15'
department:
- _id: MiLe
- _id: TaHa
doi: 10.1103/PhysRevB.108.045115
ec_funded: 1
external_id:
arxiv:
- '2203.12666'
intvolume: ' 108'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.12666
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Diagrammatic Monte Carlo for electronic correlation in molecules: High-order
many-body perturbation theory with low scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13970'
article_processing_charge: No
article_type: original
author:
- first_name: Amiera
full_name: Madani, Amiera
last_name: Madani
- first_name: Eric T.
full_name: Sletten, Eric T.
last_name: Sletten
- first_name: Cristian
full_name: Cavedon, Cristian
last_name: Cavedon
- first_name: Peter H.
full_name: Seeberger, Peter H.
last_name: Seeberger
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
citation:
ama: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271
apa: Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B.
(2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271
chicago: Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger,
and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.
ieee: A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,”
Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.
ista: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 100, 271–286.
mla: Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.
short: A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses
100 (2023) 271–286.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-07T08:21:45Z
day: '01'
department:
- _id: BaPi
doi: 10.15227/orgsyn.100.0271
intvolume: ' 100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15227/orgsyn.100.0271
month: '07'
oa: 1
oa_version: Published Version
page: 271-286
publication: Organic Syntheses
publication_identifier:
eissn:
- 2333-3553
issn:
- 0078-6209
publication_status: published
publisher: Organic Syntheses
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2023'
...
---
_id: '13127'
abstract:
- lang: eng
text: Cooperative disease defense emerges as group-level collective behavior, yet
how group members make the underlying individual decisions is poorly understood.
Using garden ants and fungal pathogens as an experimental model, we derive the
rules governing individual ant grooming choices and show how they produce colony-level
hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic
modeling reveal that ants increase grooming and preferentially target highly-infectious
individuals when perceiving high pathogen load, but transiently suppress grooming
after having been groomed by nestmates. Ants thus react to both, the infectivity
of others and the social feedback they receive on their own contagiousness. While
inferred solely from momentary ant decisions, these behavioral rules quantitatively
predict hour-long experimental dynamics, and synergistically combine into efficient
colony-wide pathogen removal. Our analyses show that noisy individual decisions
based on only local, incomplete, yet dynamically-updated information on pathogen
threat and social feedback can lead to potent collective disease defense.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity
Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer
Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for
general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian
Theis and the Social Immunity Team for continued feedback throughout, and Michael
Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg
for comments on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency
of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science
Program (Grant No. RGP0065/2012) to GT.
article_number: '3232'
article_processing_charge: Yes
article_type: original
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Katarína
full_name: Bod'Ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'Ová
orcid: 0000-0002-7214-0171
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen
detection and social feedback shape collective hygiene in ants. Nature Communications.
2023;14. doi:10.1038/s41467-023-38947-y
apa: Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer,
S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene
in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y
chicago: Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik,
and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective
Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.
ieee: B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic
pathogen detection and social feedback shape collective hygiene in ants,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic
pathogen detection and social feedback shape collective hygiene in ants. Nature
Communications. 14, 3232.
mla: Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232,
Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
short: B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature
Communications 14 (2023).
date_created: 2023-06-11T22:00:40Z
date_published: 2023-06-03T00:00:00Z
date_updated: 2023-08-07T13:09:09Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
- _id: GaTk
doi: 10.1038/s41467-023-38947-y
ec_funded: 1
external_id:
isi:
- '001002562700005'
pmid:
- '37270641'
file:
- access_level: open_access
checksum: 4af0393e3ed47b3fc46e68b81c3c1007
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project:
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call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
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grant_number: RGP0065/2012
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publication_identifier:
eissn:
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title: Dynamic pathogen detection and social feedback shape collective hygiene in
ants
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '12945'
abstract:
- lang: eng
text: "basic data for use in code for experimental data analysis for manuscript
under revision: \r\nDynamic pathogen detection and social feedback shape collective
hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S"
acknowledged_ssus:
- _id: LifeSc
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the
Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program
(Grant No. RGP0065/2012) to GT.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape
collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945'
apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback
shape collective hygiene in ants” . Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:12945'
chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:12945.'
ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape
collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.'
ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback
shape collective hygiene in ants’ , Institute of Science and Technology Austria,
10.15479/AT:ISTA:12945.'
mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria,
2023, doi:10.15479/AT:ISTA:12945.'
short: S. Cremer, (2023).
contributor:
- contributor_type: data_collector
first_name: Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- contributor_type: data_collector
first_name: Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- contributor_type: researcher
first_name: Katarina
last_name: Bodova
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
date_created: 2023-05-11T21:35:17Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2023-08-07T13:09:09Z
day: '12'
ddc:
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department:
- _id: SyCr
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keyword:
- collective behavior
- host-pathogen interactions
- social immunity
- epidemiology
- social insects
- probabilistic modeling
month: '05'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
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status: public
title: 'Data from: "Dynamic pathogen detection and social feedback shape collective
hygiene in ants" '
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image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
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year: '2023'
...
---
_id: '12885'
abstract:
- lang: eng
text: 'High-performance semiconductors rely upon precise control of heat and charge
transport. This can be achieved by precisely engineering defects in polycrystalline
solids. There are multiple approaches to preparing such polycrystalline semiconductors,
and the transformation of solution-processed colloidal nanoparticles is appealing
because colloidal nanoparticles combine low cost with structural and compositional
tunability along with rich surface chemistry. However, the multiple processes
from nanoparticle synthesis to the final bulk nanocomposites are very complex.
They involve nanoparticle purification, post-synthetic modifications, and finally
consolidation (thermal treatments and densification). All these properties dictate
the final material’s composition and microstructure, ultimately affecting its
functional properties. This thesis explores the synthesis, surface chemistry and
consolidation of colloidal semiconductor nanoparticles into dense solids. In particular,
the transformations that take place during these processes, and their effect on
the material’s transport properties are evaluated. '
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
citation:
ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation.
2023. doi:10.15479/at:ista:12885'
apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885'
chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.'
ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to
consolidation,” Institute of Science and Technology Austria, 2023.'
ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria.'
mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.'
short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to
Consolidation, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-02T07:58:57Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-08-14T07:25:26Z
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ddc:
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department:
- _id: GradSch
- _id: MaIb
doi: 10.15479/at:ista:12885
ec_funded: 1
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oa: 1
oa_version: Published Version
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project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-028-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
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relation: part_of_dissertation
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relation: part_of_dissertation
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status: public
supervisor:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12087'
abstract:
- lang: eng
text: Following up on the recent work on lower Ricci curvature bounds for quantum
systems, we introduce two noncommutative versions of curvature-dimension bounds
for symmetric quantum Markov semigroups over matrix algebras. Under suitable such
curvature-dimension conditions, we prove a family of dimension-dependent functional
inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power
in the noncommutative setting. We also provide examples satisfying certain curvature-dimension
conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers
over group algebras and generalized depolarizing semigroups.
acknowledgement: H.Z. is supported by the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411
and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges
support from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (Grant Agreement No. 716117) and from the
Austrian Science Fund (FWF) through grant number F65. Both authors would like to
thank Jan Maas for fruitful discussions and helpful comments. Open access funding
provided by Austrian Science Fund (FWF).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov
semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x
apa: Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric
quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x
chicago: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for
Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer
Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x.
ieee: M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum
Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp.
717–750, 2023.
ista: Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum
Markov semigroups. Annales Henri Poincare. 24, 717–750.
mla: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric
Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.
short: M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.
date_created: 2022-09-11T22:01:57Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:39:28Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00023-022-01220-x
ec_funded: 1
external_id:
arxiv:
- '2105.08303'
isi:
- '000837499800002'
file:
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checksum: 8c7b185eba5ccd92ef55c120f654222c
content_type: application/pdf
creator: dernst
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file_size: 554871
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success: 1
file_date_updated: 2023-08-14T11:38:28Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 717-750
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature-dimension conditions for symmetric quantum Markov semigroups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '9652'
abstract:
- lang: eng
text: In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated
nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice.
We study weaker notions of equivalence of separated nets and demonstrate that
such notions also give rise to distinct equivalence classes. Put differently,
we find occurrences of particularly strong divergence of separated nets from the
integer lattice. Our approach generalises that of Burago and Kleiner and McMullen
which takes place largely in a continuous setting. Existence of irregular separated
nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞).
In the present work we obtain stronger types of non-realisable densities.
acknowledgement: 'This work was done while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics.
2023;253:501-554. doi:10.1007/s11856-022-2448-6
apa: Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel
Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6
chicago: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.”
Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.
ieee: M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal
of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.
ista: Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal
of Mathematics. 253, 501–554.
mla: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel
Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.
short: M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.
date_created: 2021-07-14T07:01:28Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:26:34Z
day: '01'
ddc:
- '515'
- '516'
department:
- _id: UlWa
doi: 10.1007/s11856-022-2448-6
external_id:
arxiv:
- '1903.05923'
isi:
- '000904950300003'
file:
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checksum: 6fa0a3207dd1d6467c309fd1bcc867d1
content_type: application/pdf
creator: vkaluza
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date_updated: 2021-07-14T07:41:50Z
file_id: '9653'
file_name: separated_nets.pdf
file_size: 900422
relation: main_file
file_date_updated: 2021-07-14T07:41:50Z
has_accepted_license: '1'
intvolume: ' 253'
isi: 1
keyword:
- Lipschitz
- bilipschitz
- bounded displacement
- modulus of continuity
- separated net
- non-realisable density
- Burago--Kleiner construction
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 501-554
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly irregular separated nets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 253
year: '2023'
...
---
_id: '10173'
abstract:
- lang: eng
text: We study the large scale behavior of elliptic systems with stationary random
coefficient that have only slowly decaying correlations. To this aim we analyze
the so-called corrector equation, a degenerate elliptic equation posed in the
probability space. In this contribution, we use a parabolic approach and optimally
quantify the time decay of the semigroup. For the theoretical point of view, we
prove an optimal decay estimate of the gradient and flux of the corrector when
spatially averaged over a scale R larger than 1. For the numerical point of view,
our results provide convenient tools for the analysis of various numerical methods.
acknowledgement: "I would like to thank my advisor Antoine Gloria for suggesting this
problem to me, as well for many interesting discussions and suggestions.\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nicolas
full_name: Clozeau, Nicolas
id: fea1b376-906f-11eb-847d-b2c0cf46455b
last_name: Clozeau
citation:
ama: 'Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields. Stochastics and Partial Differential Equations:
Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w'
apa: 'Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic
homogenization for correlated coefficient fields. Stochastics and Partial
Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w'
chicago: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic
Homogenization for Correlated Coefficient Fields.” Stochastics and Partial
Differential Equations: Analysis and Computations. Springer Nature, 2023.
https://doi.org/10.1007/s40072-022-00254-w.'
ieee: 'N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields,” Stochastics and Partial Differential Equations:
Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.'
ista: 'Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields. Stochastics and Partial Differential Equations:
Analysis and Computations. 11, 1254–1378.'
mla: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic
Homogenization for Correlated Coefficient Fields.” Stochastics and Partial
Differential Equations: Analysis and Computations, vol. 11, Springer Nature,
2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.'
short: 'N. Clozeau, Stochastics and Partial Differential Equations: Analysis and
Computations 11 (2023) 1254–1378.'
date_created: 2021-10-23T10:50:22Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-14T11:51:47Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s40072-022-00254-w
external_id:
arxiv:
- '2102.07452'
isi:
- '000799715600001'
file:
- access_level: open_access
checksum: f83dcaecdbd3ace862c4ed97a20e8501
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:51:04Z
date_updated: 2023-08-14T11:51:04Z
file_id: '14052'
file_name: 2023_StochPartialDiffEquations_Clozeau.pdf
file_size: 1635193
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:51:04Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1254–1378
publication: 'Stochastics and Partial Differential Equations: Analysis and Computations'
publication_identifier:
issn:
- 2194-0401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal decay of the parabolic semigroup in stochastic homogenization for
correlated coefficient fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '11741'
abstract:
- lang: eng
text: Following E. Wigner’s original vision, we prove that sampling the eigenvalue
gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the
celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly,
we prove universality for a monoparametric family of deformed Wigner matrices
H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just
using the randomness of a single scalar real random variable x. Both results constitute
quenched versions of bulk universality that has so far only been proven in annealed
sense with respect to the probability space of the matrix ensemble.
acknowledgement: "The authors are indebted to Sourav Chatterjee for forwarding the
very inspiring question that Stephen Shenker originally addressed to him which initiated
the current paper. They are also grateful that the authors of [23] kindly shared
their preliminary numerical results in June 2021.\r\nOpen access funding provided
by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner
matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality
for deformed Wigner matrices. Probability Theory and Related Fields. Springer
Nature. https://doi.org/10.1007/s00440-022-01156-7
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality
for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer
Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed
Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer
Nature, pp. 1183–1218, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed
Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.
mla: Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.”
Probability Theory and Related Fields, vol. 185, Springer Nature, 2023,
pp. 1183–1218, doi:10.1007/s00440-022-01156-7.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields
185 (2023) 1183–1218.
date_created: 2022-08-07T22:02:00Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-14T12:48:09Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00440-022-01156-7
external_id:
arxiv:
- '2106.10200'
isi:
- '000830344500001'
file:
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checksum: b9247827dae5544d1d19c37abe547abc
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creator: dernst
date_created: 2023-08-14T12:47:32Z
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language:
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oa: 1
oa_version: Published Version
page: 1183–1218
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- 1432-2064
issn:
- 0178-8051
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quenched universality for deformed Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 185
year: '2023'
...
---
_id: '12331'
abstract:
- lang: eng
text: High carrier mobility is critical to improving thermoelectric performance
over a broad temperature range. However, traditional doping inevitably deteriorates
carrier mobility. Herein, we develop a strategy for fine tuning of defects to
improve carrier mobility. To begin, n-type PbTe is created by compensating for
the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering,
resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is
introduced to compensate for the remaining intrinsic Pb vacancies. We find that
excess Ag exhibits a dynamic doping process with increasing temperatures, increasing
both the carrier concentration and carrier mobility throughout a wide temperature
range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained
for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier
concentration suppresses the bipolar thermal conductivity at high temperatures.
The final step is using iodine to optimize the carrier concentration to ∼1019
cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of
∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings
demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance
carrier mobility and improve thermoelectric performance.
acknowledgement: The National Key Research and Development Program of China (2018YFA0702100),
the Basic Science Center Project of the National Natural Science Foundation of China
(51788104), the National Natural Science Foundation of China (51571007 and 51772012),
the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the
National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise
Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Siqi
full_name: Wang, Siqi
last_name: Wang
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Shulin
full_name: Bai, Shulin
last_name: Bai
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Yingcai
full_name: Zhu, Yingcai
last_name: Zhu
- first_name: Shaoping
full_name: Zhan, Shaoping
last_name: Zhan
- first_name: Junqing
full_name: Zheng, Junqing
last_name: Zheng
- first_name: Shuwei
full_name: Tang, Shuwei
last_name: Tang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier
mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry
of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542
apa: Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023).
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. American Chemical Society.
https://doi.org/10.1021/acs.chemmater.2c03542
chicago: Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping
Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables
High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.”
Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.
ieee: S. Wang et al., “Fine tuning of defects enables high carrier mobility
and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials,
vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.
ista: Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023.
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.
mla: Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and
Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials,
vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.
short: S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D.
Zhao, Chemistry of Materials 35 (2023) 755–763.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-01-24T00:00:00Z
date_updated: 2023-08-14T12:57:44Z
day: '24'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acs.chemmater.2c03542
external_id:
isi:
- '000914749700001'
file:
- access_level: open_access
checksum: b21dca2aa7a80c068bc256bdd1fea9df
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T12:57:25Z
date_updated: 2023-08-14T12:57:25Z
file_id: '14055'
file_name: 2023_ChemistryMaterials_Wang.pdf
file_size: 2961043
relation: main_file
success: 1
file_date_updated: 2023-08-14T12:57:25Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 755-763
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Chemistry of Materials
publication_identifier:
eissn:
- 1520-5002
issn:
- 0897-4756
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '11999'
abstract:
- lang: eng
text: 'A simple drawing D(G) of a graph G is one where each pair of edges share
at most one point: either a common endpoint or a proper crossing. An edge e in
the complement of G can be inserted into D(G) if there exists a simple drawing
of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is
rectilinear (pseudolinear), that is, the edges can be extended into an arrangement
of lines (pseudolines), then any edge in the complement of G can be inserted.
In contrast, we show that it is NP-complete to decide whether one edge can be
inserted into a simple drawing. This remains true even if we assume that the drawing
is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles.
On the positive side, we show that, given an arrangement of pseudocircles A and
a pseudosegment σ, it can be decided in polynomial time whether there exists a
pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.'
acknowledgement: 'This work was started during the 6th Austrian–Japanese–Mexican–Spanish
Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants
for the good atmosphere as well as discussions on the topic. Also, we thank Jan
Kynčl for sending us remarks on a preliminary version of this work and an anonymous
referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie
grant agreement No 754411. Fabian Klute was partially supported by the Netherlands
Organisation for Scientific Research (NWO) under project no. 612.001.651 and by
the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were
partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative
DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was
also partially supported by the Independent Research Fund Denmark grant 2020-2023
(9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded
by the Ministry of Universities of Spain and the European Union (NextGenerationEU).
Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Fabian
full_name: Klute, Fabian
last_name: Klute
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
- first_name: Birgit
full_name: Vogtenhuber, Birgit
last_name: Vogtenhuber
- first_name: Raimund
full_name: Seidel, Raimund
last_name: Seidel
- first_name: Tilo
full_name: Wiedera, Tilo
last_name: Wiedera
citation:
ama: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting
one edge into a simple drawing is hard. Discrete and Computational Geometry.
2023;69:745–770. doi:10.1007/s00454-022-00394-9
apa: Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R.,
& Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9
chicago: Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber,
Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is
Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.
ieee: A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and
T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and
Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.
ista: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T.
2023. Inserting one edge into a simple drawing is hard. Discrete and Computational
Geometry. 69, 745–770.
mla: Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is
Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023,
pp. 745–770, doi:10.1007/s00454-022-00394-9.
short: A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera,
Discrete and Computational Geometry 69 (2023) 745–770.
date_created: 2022-08-28T22:02:01Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-14T12:51:25Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/s00454-022-00394-9
ec_funded: 1
external_id:
arxiv:
- '1909.07347'
isi:
- '000840292800001'
file:
- access_level: open_access
checksum: def7ae3b28d9fd6aec16450e40090302
content_type: application/pdf
creator: alisjak
date_created: 2022-08-29T11:23:15Z
date_updated: 2022-08-29T11:23:15Z
file_id: '12006'
file_name: 2022_DiscreteandComputionalGeometry_Arroyo.pdf
file_size: 1002218
relation: main_file
success: 1
file_date_updated: 2022-08-29T11:23:15Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 745–770
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inserting one edge into a simple drawing is hard
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2023'
...
---
_id: '12330'
abstract:
- lang: eng
text: 'The design and implementation of efficient concurrent data structures has
seen significant attention. However, most of this work has focused on concurrent
data structures providing good worst-case guarantees, although, in real workloads,
objects are often accessed at different rates. Efficient distribution-adaptive
data structures, such as splay-trees, are known in the sequential case; however,
they often are hard to translate efficiently to the concurrent case. We investigate
distribution-adaptive concurrent data structures, and propose a new design called
the splay-list. At a high level, the splay-list is similar to a standard skip-list,
with the key distinction that the height of each element adapts dynamically to
its access rate: popular elements “move up,” whereas rarely-accessed elements
decrease in height. We show that the splay-list provides order-optimal amortized
complexity bounds for a subset of operations, while being amenable to efficient
concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity
for performance, and can outperform the only previously-known distribution-adaptive
concurrent design in certain workloads.'
article_processing_charge: No
article_type: original
author:
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Alexandra
full_name: Drozdova, Alexandra
last_name: Drozdova
- first_name: Amirkeivan
full_name: Mohtashami, Amirkeivan
last_name: Mohtashami
citation:
ama: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive
concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x'
apa: 'Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The
splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00441-x'
chicago: 'Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan
Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.'
ieee: 'V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list:
A distribution-adaptive concurrent skip-list,” Distributed Computing, vol.
36. Springer Nature, pp. 395–418, 2023.'
ista: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list:
A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.'
mla: 'Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent
Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp.
395–418, doi:10.1007/s00446-022-00441-x.'
short: V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing
36 (2023) 395–418.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-14T12:54:32Z
day: '01'
department:
- _id: DaAl
doi: 10.1007/s00446-022-00441-x
external_id:
arxiv:
- '2008.01009'
isi:
- '000913424000001'
intvolume: ' 36'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01009
month: '09'
oa: 1
oa_version: Preprint
page: 395-418
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The splay-list: A distribution-adaptive concurrent skip-list'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12114'
abstract:
- lang: eng
text: 'Probing the dynamics of aromatic side chains provides important insights
into the behavior of a protein because flips of aromatic rings in a protein’s
hydrophobic core report on breathing motion involving a large part of the protein.
Inherently invisible to crystallography, aromatic motions have been primarily
studied by solution NMR. The question how packing of proteins in crystals affects
ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning
NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a
protein in three different crystal packing environments to shed light onto possible
impact of packing on ring flips. The flips of the two Phe residues in ubiquitin,
both surface exposed, appear remarkably conserved in the different crystal forms,
even though the intermolecular packing is quite different: Phe4 flips on a ca.
10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to
µs motion. Our findings suggest that intramolecular influences are more important
for ring flips than intermolecular (packing) effects.'
acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within
the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche)
CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research
Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the
Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI
(ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership
for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing
and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg
State University in a form of the grant 92425251 and the access to the MRR, MCT
and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact
that “tensor asymmetry” is better called “tensor biaxiality”.
article_number: '100079'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Olga O.
full_name: Lebedenko, Olga O.
last_name: Lebedenko
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079'
apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R.,
Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079'
chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman
Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in
Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal
of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.'
ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin
protein crystals from MAS NMR and MD,” Journal of Structural Biology: X,
vol. 7. Elsevier, 2023.'
ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR,
Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals
from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.'
mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin
Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X,
vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.'
short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R.
Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).'
date_created: 2023-01-12T11:55:38Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-16T09:37:25Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.yjsbx.2022.100079
external_id:
pmid:
- '36578472'
file:
- access_level: open_access
checksum: b4b1c10a31018aafe053b7d55a470e54
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T09:36:28Z
date_updated: 2023-08-16T09:36:28Z
file_id: '14064'
file_name: 2023_JourStrucBiologyX_Gauto.pdf
file_size: 5132322
relation: main_file
success: 1
file_date_updated: 2023-08-16T09:36:28Z
has_accepted_license: '1'
intvolume: ' 7'
keyword:
- Structural Biology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Structural Biology: X'
publication_identifier:
issn:
- 2590-1524
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS
NMR and MD
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12163'
abstract:
- lang: eng
text: Small GTPases play essential roles in the organization of eukaryotic cells.
In recent years, it has become clear that their intracellular functions result
from intricate biochemical networks of the GTPase and their regulators that dynamically
bind to a membrane surface. Due to the inherent complexities of their interactions,
however, revealing the underlying mechanisms of action is often difficult to achieve
from in vivo studies. This review summarizes in vitro reconstitution approaches
developed to obtain a better mechanistic understanding of how small GTPase activities
are regulated in space and time.
acknowledgement: The authors acknowledge support from IST Austria and helpful comments
from the anonymous reviewers that helped to improve this manuscript. We apologize
to the authors of primary literature and outstanding research not cited here due
to space restraints.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: Hanifatul R
full_name: Budiman, Hanifatul R
id: 55380f95-15b2-11ec-abd3-aff8e230696b
last_name: Budiman
- first_name: Lukasz M
full_name: Kowalski, Lukasz M
id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2
last_name: Kowalski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
citation:
ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro
reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777.
doi:10.1002/1873-3468.14540
apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic,
I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters.
Wiley. https://doi.org/10.1002/1873-3468.14540
chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz
M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.
ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic,
“In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol.
597, no. 6. Wiley, pp. 762–777, 2023.
ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In
vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.
mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.
short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic,
FEBS Letters 597 (2023) 762–777.
date_created: 2023-01-12T12:09:58Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:32:29Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1002/1873-3468.14540
external_id:
isi:
- '000891573000001'
pmid:
- '36448231'
file:
- access_level: open_access
checksum: 7492244d3f9c5faa1347ef03f6e5bc84
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:31:04Z
date_updated: 2023-08-16T08:31:04Z
file_id: '14063'
file_name: 2023_FEBSLetters_Loose.pdf
file_size: 3148143
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:31:04Z
has_accepted_license: '1'
intvolume: ' 597'
isi: 1
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Biology
- Biochemistry
- Structural Biology
- Biophysics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 762-777
pmid: 1
publication: FEBS Letters
publication_identifier:
eissn:
- 1873-3468
issn:
- 0014-5793
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution of small GTPase regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 597
year: '2023'
...
---
_id: '12164'
abstract:
- lang: eng
text: 'A shared-memory counter is a widely-used and well-studied concurrent object.
It supports two operations: An Inc operation that increases its value by 1 and
a Read operation that returns its current value. In Jayanti et al (SIAM J Comput,
30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case
step complexity of obstruction-free implementations, from read-write registers,
of a large class of shared objects that includes counters. The lower bound leaves
open the question of finding counter implementations with sub-linear amortized
step complexity. In this work, we address this gap. We show that n-process, wait-free
and linearizable counters can be implemented from read-write registers with O(log2n)
amortized step complexity. This is the first counter algorithm from read-write
registers that provides sub-linear amortized step complexity in executions of
arbitrary length. Since a logarithmic lower bound on the amortized step complexity
of obstruction-free counter implementations exists, our upper bound is within
a logarithmic factor of the optimal. The worst-case step complexity of the construction
remains linear, which is optimal. This is obtained thanks to a new max register
construction with O(logn) amortized step complexity in executions of arbitrary
length in which the value stored in the register does not grow too quickly. We
then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel
[1] in which we “plug” our max register implementation to show that it remains
linearizable while achieving O(log2n) amortized step complexity.'
acknowledgement: A preliminary version of this work appeared in DISC’19. Mirza Ahad
Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes
and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported
by the Israel Science Foundation (Grants 380/18 and 1425/22).
article_processing_charge: No
article_type: original
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Danny
full_name: Hendler, Danny
last_name: Hendler
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5
apa: Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived
counters with polylogarithmic amortized step complexity. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00439-5
chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers.
“Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.
ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with
polylogarithmic amortized step complexity,” Distributed Computing, vol.
36. Springer Nature, pp. 29–43, 2023.
ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 36, 29–43.
mla: Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized
Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023,
pp. 29–43, doi:10.1007/s00446-022-00439-5.
short: M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023)
29–43.
date_created: 2023-01-12T12:10:08Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:39:36Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00446-022-00439-5
external_id:
isi:
- '000890138700001'
intvolume: ' 36'
isi: 1
keyword:
- Computational Theory and Mathematics
- Computer Networks and Communications
- Hardware and Architecture
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/
month: '03'
oa: 1
oa_version: Preprint
page: 29-43
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived counters with polylogarithmic amortized step complexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12515'
abstract:
- lang: eng
text: "Introduction: The olfactory system in most mammals is divided into several
subsystems based on the anatomical locations of the neuroreceptor cells involved
and the receptor families that are expressed. In addition to the main olfactory
system and the vomeronasal system, a range of olfactory subsystems converge onto
the transition zone located between the main olfactory bulb (MOB) and the accessory
olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL
contains specialized glomeruli that receive noncanonical sensory afferences and
which interact with the MOB and AOB. Little is known regarding the olfactory subsystems
of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing
the OL in the red fox by performing general and specific histological stainings
on serial sections, using both single and double immunohistochemical and lectin-histochemical
labeling techniques.\r\nResults: As a result, we have been able to determine that
the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development
and complexity.\r\nDiscussion: This makes this species a novel mammalian model,
the study of which could improve our understanding of the noncanonical pathways
involved in the processing of chemosensory cues."
acknowledgement: This work was partially supported by a grant from “Consello Social
Universidade de Santiago de Compostela” 2022-PU004.We would like to show special
gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing
us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia,
Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación
Galega de Caza for providing the red foxes used in this study.
article_number: '1097467'
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Ortiz-Leal, Irene
last_name: Ortiz-Leal
- first_name: Mateo V.
full_name: Torres, Mateo V.
last_name: Torres
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Luis Eusebio
full_name: Fidalgo, Luis Eusebio
last_name: Fidalgo
- first_name: Ana María
full_name: López-Beceiro, Ana María
last_name: López-Beceiro
- first_name: Jorge A.
full_name: Larriva-Sahd, Jorge A.
last_name: Larriva-Sahd
- first_name: Pablo
full_name: Sánchez-Quinteiro, Pablo
last_name: Sánchez-Quinteiro
citation:
ama: Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of
the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb
pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467
apa: Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro,
A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory
limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory
bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467
chicago: Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio
Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro.
“The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a
Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers,
2023. https://doi.org/10.3389/fnana.2022.1097467.
ieee: I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes
vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers
in Neuroanatomy, vol. 16. Frontiers, 2023.
ista: Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM,
Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox
(Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway.
Frontiers in Neuroanatomy. 16, 1097467.
mla: Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes).
New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in
Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.
short: I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro,
J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).
date_created: 2023-02-05T23:01:00Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-16T11:37:52Z
day: '10'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.3389/fnana.2022.1097467
external_id:
isi:
- '000919786900001'
pmid:
- '36704406'
file:
- access_level: open_access
checksum: 49cd40f3bda6f267079427042e7d15e3
content_type: application/pdf
creator: dernst
date_created: 2023-02-06T07:56:14Z
date_updated: 2023-02-06T07:56:14Z
file_id: '12518'
file_name: 2022_FrontiersNeuroanatomy_OrtizLeal.pdf
file_size: 21943473
relation: main_file
success: 1
file_date_updated: 2023-02-06T07:56:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neuroanatomy
publication_identifier:
eissn:
- 1662-5129
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding
a noncanonical olfactory bulb pathway
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-16T11:32:33Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
external_id:
isi:
- '000909067600003'
file:
- access_level: open_access
checksum: 668447a1c8d360b68f8aaf9e08ed644f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:30:45Z
date_updated: 2023-08-16T11:30:45Z
file_id: '14066'
file_name: 2023_NatureBioTech_Yeung.pdf
file_size: 12040976
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:30:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2023'
...
---
_id: '12183'
abstract:
- lang: eng
text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with
Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii
regime, with an optimal bound on the condensate depletion. Moreover, our lower
bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann
bracketing) a lower bound for the ground state energy of N bosons in a large box
[−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions.
Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3
apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann
boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3
chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.
ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary
conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560,
2023.
ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary
conditions. Annales Henri Poincare. 24, 1505–1560.
mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.
short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.
date_created: 2023-01-15T23:00:52Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-16T11:34:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-022-01252-3
ec_funded: 1
external_id:
arxiv:
- '2205.15284'
isi:
- '000910751800002'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.15284
month: '05'
oa: 1
oa_version: Preprint
page: 1505-1560
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bose Gas in a box with Neumann boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12544'
abstract:
- lang: eng
text: Geometry is crucial in our efforts to comprehend the structures and dynamics
of biomolecules. For example, volume, surface area, and integrated mean and Gaussian
curvature of the union of balls representing a molecule are used to quantify its
interactions with the water surrounding it in the morphometric implicit solvent
models. The Alpha Shape theory provides an accurate and reliable method for computing
these geometric measures. In this paper, we derive homogeneous formulas for the
expressions of these measures and their derivatives with respect to the atomic
coordinates, and we provide algorithms that implement them into a new software
package, AlphaMol. The only variables in these formulas are the interatomic distances,
making them insensitive to translations and rotations. AlphaMol includes a sequential
algorithm and a parallel algorithm. In the parallel version, we partition the
atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree
algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented
by a buffer zone to account for atoms whose ball representations may partially
cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up
compared to an independent serial implementation when using 32 processors. For
instance, it takes 31 s to compute the geometric measures and derivatives of each
atom in a viral capsid with more than 26 million atoms on 32 Intel processors
running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant
computations, which ultimately limit the impact of using multiple processors.
AlphaMol is available as an OpenSource software.
acknowledgement: "P.K. acknowledges support from the University of California Multicampus
Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant
No.1760485). H.E. acknowledges support from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program, Grant No.
788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31,
and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access
is funded by the Austrian Science Fund (FWF)."
article_processing_charge: No
article_type: original
author:
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean,
and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346
apa: Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume,
surface area, mean, and Gaussian curvatures of molecules and their derivatives.
Journal of Chemical Information and Modeling. American Chemical Society.
https://doi.org/10.1021/acs.jcim.2c01346
chicago: Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the
Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.”
Journal of Chemical Information and Modeling. American Chemical Society,
2023. https://doi.org/10.1021/acs.jcim.2c01346.
ieee: P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface
area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal
of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society,
pp. 973–985, 2023.
ista: Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area,
mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 63(3), 973–985.
mla: Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian
Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information
and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85,
doi:10.1021/acs.jcim.2c01346.
short: P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and
Modeling 63 (2023) 973–985.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-02-13T00:00:00Z
date_updated: 2023-08-16T12:22:07Z
day: '13'
ddc:
- '510'
- '540'
department:
- _id: HeEd
doi: 10.1021/acs.jcim.2c01346
ec_funded: 1
external_id:
isi:
- '000920370700001'
pmid:
- '36638318'
file:
- access_level: open_access
checksum: 7d20562269edff1e31b9d6019d4983b0
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:21:13Z
date_updated: 2023-08-16T12:21:13Z
file_id: '14070'
file_name: 2023_JCIM_Koehl.pdf
file_size: 8069223
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:21:13Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 973-985
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Journal of Chemical Information and Modeling
publication_identifier:
eissn:
- 1549-960X
issn:
- 1549-9596
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the volume, surface area, mean, and Gaussian curvatures of molecules
and their derivatives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2023'
...
---
_id: '12543'
abstract:
- lang: eng
text: Treating sick group members is a hallmark of collective disease defence in
vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness
and epidemiology, it is still largely unknown how pathogens react to the selection
pressure imposed by care intervention. Using social insects and pathogenic fungi,
we here performed a serial passage experiment in the presence or absence of colony
members, which provide social immunity by grooming off infectious spores from
exposed individuals. We found specific effects on pathogen diversity, virulence
and transmission. Under selection of social immunity, pathogens invested into
higher spore production, but spores were less virulent. Notably, they also elicited
a lower grooming response in colony members, compared with spores from the individual
host selection lines. Chemical spore analysis suggested that the spores from social
selection lines escaped the caregivers’ detection by containing lower levels of
ergosterol, a key fungal membrane component. Experimental application of chemically
pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated
cue triggering host social immunity against fungal pathogens. By reducing this
detection cue, pathogens were able to evade the otherwise very effective collective
disease defences of their social hosts.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the
fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team
at ISTA for ant collection and experimental help, in particular H. Leitner, and
the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg
and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the
Social Immunity team for comments on the manuscript. The study was funded by the
German Research Foundation (CR118/3-1) within the Framework of the Priority Program
SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon
2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Michaela
full_name: Hönigsberger, Michaela
id: 953894f3-25bd-11ec-8556-f70a9d38ef60
last_name: Hönigsberger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Niklas
full_name: Kampleitner, Niklas
id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87
last_name: Kampleitner
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6
apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F.,
Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature
Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6
chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse,
Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt,
and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and
Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.
ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology
and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.
ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner
N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 7, 450–460.
mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology
and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.
short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N.
Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution
7 (2023) 450–460.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T11:55:48Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
- _id: LifeSc
- _id: JiFr
doi: 10.1038/s41559-023-01981-6
ec_funded: 1
external_id:
isi:
- '000924572800001'
pmid:
- '36732670'
file:
- access_level: open_access
checksum: 8244f4650a0e7aeea488d1bcd4a31702
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:54:59Z
date_updated: 2023-08-16T11:54:59Z
file_id: '14069'
file_name: 2023_NatureEcoEvo_Stock.pdf
file_size: 1600499
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:54:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 450-460
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Nature Ecology and Evolution
publication_identifier:
eissn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/
scopus_import: '1'
status: public
title: Pathogen evasion of social immunity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-16T11:44:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
- '001021692200001'
pmid:
- '37065438'
file:
- access_level: open_access
checksum: a240a041cb9b9b7c8ba93a4706674a3f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:43:33Z
date_updated: 2023-08-16T11:43:33Z
file_id: '14068'
file_name: 2023_EvLetters_Mrnjavac.pdf
file_size: 2592189
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:43:33Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12679'
abstract:
- lang: eng
text: How to generate a brain of correct size and with appropriate cell-type diversity
during development is a major question in Neuroscience. In the developing neocortex,
radial glial progenitor (RGP) cells are the main neural stem cells that produce
cortical excitatory projection neurons, glial cells, and establish the prospective
postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated
developmental program that when disrupted can result in severe cortical malformations
such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms
instructing faithful RGP lineage progression are however not well understood.
This review will summarize recent conceptual advances that contribute to our understanding
of the general principles of RGP lineage progression.
acknowledgement: "I wish to thank all current and past members of the Hippenmeyer
laboratory at ISTA for exciting discussions on the subject of this review. I apologize
to colleagues whose work I could not cite and/or discuss in the frame of the available
space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported
by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council
(ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(grant agree-ment no. 725780 LinPro) to SH."
article_number: '102695'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Hippenmeyer S. Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4).
doi:10.1016/j.conb.2023.102695'
apa: 'Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology.
Elsevier. https://doi.org/10.1016/j.conb.2023.102695'
chicago: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression:
Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology.
Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.'
ieee: 'S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex,” Current Opinion in Neurobiology, vol.
79, no. 4. Elsevier, 2023.'
ista: 'Hippenmeyer S. 2023. Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4),
102695.'
mla: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights
from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol.
79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.'
short: S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).
date_created: 2023-02-26T12:24:21Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T12:30:25Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.conb.2023.102695
ec_funded: 1
external_id:
isi:
- '000953497700001'
pmid:
- '36842274'
file:
- access_level: open_access
checksum: 4d11c4ca87e6cbc4d2ac46d3225ea615
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:29:06Z
date_updated: 2023-08-16T12:29:06Z
file_id: '14071'
file_name: 2023_CurrentOpinionNeurobio_Hippenmeyer.pdf
file_size: 1787894
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:29:06Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '4'
keyword:
- General Neuroscience
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Principles of neural stem cell lineage progression: Insights from developing
cerebral cortex'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2023'
...
---
_id: '12429'
abstract:
- lang: eng
text: In this paper, we consider traces at initial times for functions with mixed
time-space smoothness. Such results are often needed in the theory of evolution
equations. Our result extends and unifies many previous results. Our main improvement
is that we can allow general interpolation couples. The abstract results are applied
to regularity problems for fractional evolution equations and stochastic evolution
equations, where uniform trace estimates on the half-line are shown.
acknowledgement: The first author has been partially supported by the Nachwuchsring—Network
for the promotion of young scientists—at TU Kaiserslautern. The second and third
authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation
for Scientific Research (NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Nick
full_name: Lindemulder, Nick
last_name: Lindemulder
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350.
doi:10.1002/mana.202100192
apa: Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding
and its applications to evolution equations. Mathematische Nachrichten.
Wiley. https://doi.org/10.1002/mana.202100192
chicago: Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding
and Its Applications to Evolution Equations.” Mathematische Nachrichten.
Wiley, 2023. https://doi.org/10.1002/mana.202100192.
ieee: A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its
applications to evolution equations,” Mathematische Nachrichten, vol. 296,
no. 4. Wiley, pp. 1319–1350, 2023.
ista: Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.
mla: Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution
Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp.
1319–50, doi:10.1002/mana.202100192.
short: A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023)
1319–1350.
date_created: 2023-01-29T23:00:59Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T11:41:42Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1002/mana.202100192
external_id:
arxiv:
- '2104.05063'
isi:
- '000914134900001'
file:
- access_level: open_access
checksum: 6f099f1d064173784d1a27716a2cc795
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:40:02Z
date_updated: 2023-08-16T11:40:02Z
file_id: '14067'
file_name: 2023_MathNachrichten_Agresti.pdf
file_size: 449280
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:40:02Z
has_accepted_license: '1'
intvolume: ' 296'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1319-1350
publication: Mathematische Nachrichten
publication_identifier:
eissn:
- 1522-2616
issn:
- 0025-584X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the trace embedding and its applications to evolution equations
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 296
year: '2023'
...
---
_id: '12430'
abstract:
- lang: eng
text: We study the time evolution of the Nelson model in a mean-field limit in which
N nonrelativistic bosons weakly couple (with respect to the particle number) to
a positive or zero mass quantized scalar field. Our main result is the derivation
of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove
the convergence of the approximate wave function to the many-body wave function
in norm, with a convergence rate proportional to the number of corrections taken
into account in the approximation. We prove an analogous result for the unitary
propagator. As an application, we derive a simple system of partial differential
equations describing the time evolution of the first- and second-order approximations
to the one-particle reduced density matrices of the particles and the quantum
field, respectively.
article_number: '2350006'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Falconi, Marco
last_name: Falconi
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order
corrections for the regularized Nelson model. Reviews in Mathematical Physics.
2023;35(4). doi:10.1142/S0129055X2350006X
apa: Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023).
Bogoliubov dynamics and higher-order corrections for the regularized Nelson model.
Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X
chicago: Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören
P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized
Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing,
2023. https://doi.org/10.1142/S0129055X2350006X.
ieee: M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov
dynamics and higher-order corrections for the regularized Nelson model,” Reviews
in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.
ista: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics
and higher-order corrections for the regularized Nelson model. Reviews in Mathematical
Physics. 35(4), 2350006.
mla: Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for
the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35,
no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.
short: M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical
Physics 35 (2023).
date_created: 2023-01-29T23:00:59Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-16T11:47:27Z
day: '09'
department:
- _id: RoSe
doi: 10.1142/S0129055X2350006X
external_id:
arxiv:
- '2110.00458'
isi:
- '000909760300001'
intvolume: ' 35'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2110.00458'
month: '01'
oa: 1
oa_version: Preprint
publication: Reviews in Mathematical Physics
publication_identifier:
issn:
- 0129-055X
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bogoliubov dynamics and higher-order corrections for the regularized Nelson
model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T12:41:53Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2023'
...
---
_id: '14085'
abstract:
- lang: eng
text: We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow
under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed,
unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm
in general sparse graphs with arbitrarily good approximation guarantee.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic
Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for
a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz
Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There,
he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich
Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster
and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their
insightful comments."
alternative_title:
- LIPIcs
article_number: '69'
article_processing_charge: Yes
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Goranci G, Henzinger MH. Efficient data structures for incremental exact and
approximate maximum flow. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.ICALP.2023.69'
apa: 'Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for
incremental exact and approximate maximum flow. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69'
chicago: Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for
Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.
ieee: G. Goranci and M. H. Henzinger, “Efficient data structures for incremental
exact and approximate maximum flow,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Goranci G, Henzinger MH. 2023. Efficient data structures for incremental
exact and approximate maximum flow. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 69.'
mla: Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata,
Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.
short: G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:00:49Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.69
ec_funded: 1
external_id:
unknown:
- '2211.09606'
file:
- access_level: open_access
checksum: 074177e815a1656de5d4071c7a3dffa6
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:59:05Z
date_updated: 2023-08-21T06:59:05Z
file_id: '14089'
file_name: 2023_LIPIcsICALP_Goranci.pdf
file_size: 875910
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:59:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient data structures for incremental exact and approximate maximum flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14084'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We will consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor
Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log
Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts
c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²)
samples for integer-valued distributions (ignoring some second-order terms and
parameters), We show this is optimal up to logarithmic factors. We illustrate
with improved algorithms for counting connected subgraphs and perfect matchings
in a graph."
acknowledgement: We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the
Wang-Landau algorithm and its use in physics.
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In:
50th International Colloquium on Automata, Languages, and Programming.
Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72'
apa: 'Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs
distributions. In 50th International Colloquium on Automata, Languages, and
Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72'
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” In 50th International Colloquium on Automata, Languages, and
Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
in 50th International Colloquium on Automata, Languages, and Programming,
Paderborn, Germany, 2023, vol. 261.
ista: 'Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions.
50th International Colloquium on Automata, Languages, and Programming. ICALP:
International Colloquium on Automata, Languages, and Programming, LIPIcs, vol.
261, 72.'
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.
short: D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T06:49:11Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: VlKo
doi: 10.4230/LIPIcs.ICALP.2023.72
external_id:
arxiv:
- '2007.10824'
file:
- access_level: open_access
checksum: 6dee0684245bb1c524b9c955db1e933d
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:45:16Z
date_updated: 2023-08-21T06:45:16Z
file_id: '14088'
file_name: 2023_LIPIcsICALP_Harris.pdf
file_size: 917791
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:45:16Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14086'
abstract:
- lang: eng
text: "The maximization of submodular functions have found widespread application
in areas such as machine learning, combinatorial optimization, and economics,
where practitioners often wish to enforce various constraints; the matroid constraint
has been investigated extensively due to its algorithmic properties and expressive
power. Though tight approximation algorithms for general matroid constraints exist
in theory, the running times of such algorithms typically scale quadratically,
and are not practical for truly large scale settings. Recent progress has focused
on fast algorithms for important classes of matroids given in explicit form. Currently,
nearly-linear time algorithms only exist for graphic and partition matroids [Alina
Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone
submodular maximization constrained by graphic, transversal matroids, or laminar
matroids in time near-linear in the size of their representation. Our algorithms
achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate
the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the
running time of our algorithm cannot be improved within the fast continuous greedy
framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák,
2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures
that maintain bases with approximate maximum cardinality and weight under certain
element updates. These data structures need to support a weight decrease operation
and a novel Freeze operation that allows the algorithm to freeze elements (i.e.
force to be contained) in its basis regardless of future data structure operations.
For the laminar matroid, we present a new dynamic data structure using the top
tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et
al., 2005] that maintains the maximum weight basis under insertions and deletions
of elements in O(log n) time. This data structure needs to support certain subtree
query and path update operations that are performed every insertion and deletion
that are non-trivial to handle in conjunction. For the transversal matroid the
Freeze operation corresponds to requiring the data structure to keep a certain
set S of vertices matched, a property that we call S-stability. While there is
a large body of work on dynamic matching algorithms, none are S-stable and maintain
an approximate maximum weight matching under vertex updates. We give the first
such algorithm for bipartite graphs with total running time linear (up to log
factors) in the number of edges."
acknowledgement: " Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast
Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by
NSF Award 2127781."
alternative_title:
- LIPIcs
article_number: '74'
article_processing_charge: Yes
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Paul
full_name: Liu, Paul
last_name: Liu
- first_name: Jan
full_name: Vondrák, Jan
last_name: Vondrák
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
citation:
ama: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for
several classes of matroids. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74'
apa: 'Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster
submodular maximization for several classes of matroids. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74'
chicago: Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular
Maximization for Several Classes of Matroids.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.
ieee: M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization
for several classes of matroids,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization
for several classes of matroids. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: International Colloquium on Automata, Languages, and Programming,
LIPIcs, vol. 261, 74.'
mla: Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes
of Matroids.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.
short: M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:05:47Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.74
ec_funded: 1
external_id:
arxiv:
- '2305.00122'
file:
- access_level: open_access
checksum: a5eef225014e003efbfbe4830fdd23cb
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:04:36Z
date_updated: 2023-08-21T07:04:36Z
file_id: '14090'
file_name: 2023_LIPIcsICALP_HenzingerM.pdf
file_size: 930943
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:04:36Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster submodular maximization for several classes of matroids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14083'
abstract:
- lang: eng
text: "In this work we consider the list-decodability and list-recoverability of
arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable
if every radius pn Hamming ball contains less than L codewords; (p,\U0001D4C1,L)_q-list-recoverability
is a generalization where we place radius pn Hamming balls on every point of a
combinatorial rectangle with side length \U0001D4C1 and again stipulate that there
be less than L codewords.\r\nOur main contribution is to precisely calculate the
maximum value of p for which there exist infinite families of positive rate (p,\U0001D4C1,L)_q-list-recoverable
codes, the quantity we call the zero-rate threshold. Denoting this value by p_*,
we in fact show that codes correcting a p_*+ε fraction of errors must have size
O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin
bound.\" To complement this, a standard random code with expurgation construction
shows that there exist positive rate codes correcting a p_*-ε fraction of errors.
We also follow a classical proof template (typically attributed to Elias and Bassalygo)
to derive from the zero-rate threshold other tradeoffs between rate and decoding
radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin
bound boils down to demonstrating the Schur convexity of a certain function defined
on the q-simplex as well as the convexity of a univariate function derived from
it. We remark that an earlier argument claimed similar results for q-ary list-decoding;
however, we point out that this earlier proof is flawed."
acknowledgement: "Nicolas Resch: Research supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research
and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the
National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements
YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions."
alternative_title:
- LIPIcs
article_number: '99'
article_processing_charge: Yes
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99'
apa: 'Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new
capacity bounds for list-decoding and list-recovery. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99'
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” In 50th International
Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 99.'
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” 50th International Colloquium on Automata, Languages, and
Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ICALP.2023.99.
short: N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:13Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:26:01Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.4230/LIPIcs.ICALP.2023.99
external_id:
arxiv:
- '2210.07754'
file:
- access_level: open_access
checksum: a449143fec3fbebb092cb8ef3b53c226
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:23:18Z
date_updated: 2023-08-21T07:23:18Z
file_id: '14091'
file_name: 2023_LIPIcsICALP_Resch.pdf
file_size: 1141497
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:23:18Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '12922'
abstract:
- lang: eng
text: The influence of structural modifications on the catalytic activity of carbon
materials is poorly understood. A collection of carbonaceous materials with different
pore networks and high nitrogen content was characterized and used to catalyze
four reactions to deduce structure–activity relationships. The CO2 cycloaddition
and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species).
The absence of large conjugated carbon domains resulting from the introduction
of large amounts of nitrogen in the carbon network is responsible for poor redox
activity, as observed through the catalytic reduction of nitrobenzene with hydrazine
and the catalytic oxidation of 3,3′,5,5′-tetramethylbenzidine using hydroperoxide.
The material with the highest activity towards Lewis acid catalysis (in the hydrolysis
of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule
activation and presents the highest concentration of electron-poor nitrogen species.
article_number: e202211663
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Lepre, Enrico
last_name: Lepre
- first_name: Sylvain
full_name: Rat, Sylvain
last_name: Rat
- first_name: Cristian
full_name: Cavedon, Cristian
last_name: Cavedon
- first_name: Peter H.
full_name: Seeberger, Peter H.
last_name: Seeberger
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Markus
full_name: Antonietti, Markus
last_name: Antonietti
- first_name: Nieves
full_name: López‐Salas, Nieves
last_name: López‐Salas
citation:
ama: Lepre E, Rat S, Cavedon C, et al. Catalytic properties of high nitrogen content
carbonaceous materials. Angewandte Chemie International Edition. 2023;62(2).
doi:10.1002/anie.202211663
apa: Lepre, E., Rat, S., Cavedon, C., Seeberger, P. H., Pieber, B., Antonietti,
M., & López‐Salas, N. (2023). Catalytic properties of high nitrogen content
carbonaceous materials. Angewandte Chemie International Edition. Wiley.
https://doi.org/10.1002/anie.202211663
chicago: Lepre, Enrico, Sylvain Rat, Cristian Cavedon, Peter H. Seeberger, Bartholomäus
Pieber, Markus Antonietti, and Nieves López‐Salas. “Catalytic Properties of High
Nitrogen Content Carbonaceous Materials.” Angewandte Chemie International Edition.
Wiley, 2023. https://doi.org/10.1002/anie.202211663.
ieee: E. Lepre et al., “Catalytic properties of high nitrogen content carbonaceous
materials,” Angewandte Chemie International Edition, vol. 62, no. 2. Wiley,
2023.
ista: Lepre E, Rat S, Cavedon C, Seeberger PH, Pieber B, Antonietti M, López‐Salas
N. 2023. Catalytic properties of high nitrogen content carbonaceous materials.
Angewandte Chemie International Edition. 62(2), e202211663.
mla: Lepre, Enrico, et al. “Catalytic Properties of High Nitrogen Content Carbonaceous
Materials.” Angewandte Chemie International Edition, vol. 62, no. 2, e202211663,
Wiley, 2023, doi:10.1002/anie.202211663.
short: E. Lepre, S. Rat, C. Cavedon, P.H. Seeberger, B. Pieber, M. Antonietti, N.
López‐Salas, Angewandte Chemie International Edition 62 (2023).
date_created: 2023-05-08T08:28:14Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-21T09:18:12Z
day: '09'
doi: 10.1002/anie.202211663
extern: '1'
intvolume: ' 62'
issue: '2'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.202211663
month: '01'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catalytic properties of high nitrogen content carbonaceous materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2023'
...
---
_id: '13450'
abstract:
- lang: eng
text: In previous work, we identified a population of 38 cool and luminous variable
stars in the Magellanic Clouds and examined 11 in detail in order to classify
them as either Thorne–Żytkow objects (TŻOs; red supergiants with a neutron star
cores) or super-asymptotic giant branch (sAGB) stars (the most massive stars that
will not undergo core collapse). This population includes HV 2112, a peculiar
star previously considered in other works to be either a TŻO or high-mass asymptotic
giant branch (AGB) star. Here we continue this investigation, using the kinematic
and radio environments and local star formation history of these stars to place
constraints on the age of the progenitor systems and the presence of past supernovae.
These stars are not associated with regions of recent star formation, and we find
no evidence of past supernovae at their locations. Finally, we also assess the
presence of heavy elements and lithium in their spectra compared to red supergiants.
We find strong absorption in Li and s-process elements compared to RSGs in most
of the sample, consistent with sAGB nucleosynthesis, while HV 2112 shows additional
strong lines associated with TŻO nucleosynthesis. Coupled with our previous mass
estimates, the results are consistent with the stars being massive (∼4–6.5 M⊙)
or sAGB (∼6.5–12 M⊙) stars in the thermally pulsing phase, providing crucial observations
of the transition between low- and high-mass stellar populations. HV 2112 is more
ambiguous; it could either be a maximally massive sAGB star, or a TŻO if the minimum
mass for stability extends down to ≲13 M⊙.
article_number: '18'
article_processing_charge: No
article_type: original
author:
- first_name: Anna J. G.
full_name: O‘Grady, Anna J. G.
last_name: O‘Grady
- first_name: Maria R.
full_name: Drout, Maria R.
last_name: Drout
- first_name: B. M.
full_name: Gaensler, B. M.
last_name: Gaensler
- first_name: C. S.
full_name: Kochanek, C. S.
last_name: Kochanek
- first_name: Kathryn F.
full_name: Neugent, Kathryn F.
last_name: Neugent
- first_name: Carolyn L.
full_name: Doherty, Carolyn L.
last_name: Doherty
- first_name: Joshua S.
full_name: Speagle, Joshua S.
last_name: Speagle
- first_name: B. J.
full_name: Shappee, B. J.
last_name: Shappee
- first_name: Michael
full_name: Rauch, Michael
last_name: Rauch
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: Bethany
full_name: Ludwig, Bethany
last_name: Ludwig
- first_name: Todd A.
full_name: Thompson, Todd A.
last_name: Thompson
citation:
ama: O‘Grady AJG, Drout MR, Gaensler BM, et al. Cool, luminous, and highly variable
stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of
Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal.
2023;943(1). doi:10.3847/1538-4357/aca655
apa: O‘Grady, A. J. G., Drout, M. R., Gaensler, B. M., Kochanek, C. S., Neugent,
K. F., Doherty, C. L., … Thompson, T. A. (2023). Cool, luminous, and highly variable
stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of
Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal.
American Astronomical Society. https://doi.org/10.3847/1538-4357/aca655
chicago: O‘Grady, Anna J. G., Maria R. Drout, B. M. Gaensler, C. S. Kochanek, Kathryn
F. Neugent, Carolyn L. Doherty, Joshua S. Speagle, et al. “Cool, Luminous, and
Highly Variable Stars in the Magellanic Clouds. II. Spectroscopic and Environmental
Analysis of Thorne–Żytkow Object and Super-AGB Star Candidates.” The Astrophysical
Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/aca655.
ieee: A. J. G. O‘Grady et al., “Cool, luminous, and highly variable stars
in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow
object and super-AGB star candidates,” The Astrophysical Journal, vol.
943, no. 1. American Astronomical Society, 2023.
ista: O‘Grady AJG, Drout MR, Gaensler BM, Kochanek CS, Neugent KF, Doherty CL, Speagle
JS, Shappee BJ, Rauch M, Götberg YLL, Ludwig B, Thompson TA. 2023. Cool, luminous,
and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental
analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical
Journal. 943(1), 18.
mla: O‘Grady, Anna J. G., et al. “Cool, Luminous, and Highly Variable Stars in the
Magellanic Clouds. II. Spectroscopic and Environmental Analysis of Thorne–Żytkow
Object and Super-AGB Star Candidates.” The Astrophysical Journal, vol.
943, no. 1, 18, American Astronomical Society, 2023, doi:10.3847/1538-4357/aca655.
short: A.J.G. O‘Grady, M.R. Drout, B.M. Gaensler, C.S. Kochanek, K.F. Neugent, C.L.
Doherty, J.S. Speagle, B.J. Shappee, M. Rauch, Y.L.L. Götberg, B. Ludwig, T.A.
Thompson, The Astrophysical Journal 943 (2023).
date_created: 2023-08-03T10:10:12Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-08-21T12:07:05Z
day: '20'
doi: 10.3847/1538-4357/aca655
extern: '1'
external_id:
arxiv:
- '2211.12438'
intvolume: ' 943'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3847/1538-4357/aca655
month: '01'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic
and environmental analysis of Thorne–Żytkow object and super-AGB star candidates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 943
year: '2023'
...
---
_id: '13449'
abstract:
- lang: eng
text: Stars strongly impact their environment, and shape structures on all scales
throughout the universe, in a process known as "feedback." Due to the complexity
of both stellar evolution and the physics of larger astrophysical structures,
there remain many unanswered questions about how feedback operates and what we
can learn about stars by studying their imprint on the wider universe. In this
white paper, we summarize discussions from the Lorentz Center meeting "Bringing
Stellar Evolution and Feedback Together" in 2022 April and identify key areas
where further dialog can bring about radical changes in how we view the relationship
between stars and the universe they live in.
article_number: '021001'
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Geen, Sam
last_name: Geen
- first_name: Poojan
full_name: Agrawal, Poojan
last_name: Agrawal
- first_name: Paul A.
full_name: Crowther, Paul A.
last_name: Crowther
- first_name: B. W.
full_name: Keller, B. W.
last_name: Keller
- first_name: Alex
full_name: de Koter, Alex
last_name: de Koter
- first_name: Zsolt
full_name: Keszthelyi, Zsolt
last_name: Keszthelyi
- first_name: Freeke
full_name: van de Voort, Freeke
last_name: van de Voort
- first_name: Ahmad A.
full_name: Ali, Ahmad A.
last_name: Ali
- first_name: Frank
full_name: Backs, Frank
last_name: Backs
- first_name: Lars
full_name: Bonne, Lars
last_name: Bonne
- first_name: Vittoria
full_name: Brugaletta, Vittoria
last_name: Brugaletta
- first_name: Annelotte
full_name: Derkink, Annelotte
last_name: Derkink
- first_name: Sylvia
full_name: Ekström, Sylvia
last_name: Ekström
- first_name: Yvonne A.
full_name: Fichtner, Yvonne A.
last_name: Fichtner
- first_name: Luca
full_name: Grassitelli, Luca
last_name: Grassitelli
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: Erin R.
full_name: Higgins, Erin R.
last_name: Higgins
- first_name: Eva
full_name: Laplace, Eva
last_name: Laplace
- first_name: Kong
full_name: You Liow, Kong
last_name: You Liow
- first_name: Marta
full_name: Lorenzo, Marta
last_name: Lorenzo
- first_name: Anna F.
full_name: McLeod, Anna F.
last_name: McLeod
- first_name: Georges
full_name: Meynet, Georges
last_name: Meynet
- first_name: Megan
full_name: Newsome, Megan
last_name: Newsome
- first_name: G.
full_name: André Oliva, G.
last_name: André Oliva
- first_name: Varsha
full_name: Ramachandran, Varsha
last_name: Ramachandran
- first_name: Martin P.
full_name: Rey, Martin P.
last_name: Rey
- first_name: Steven
full_name: Rieder, Steven
last_name: Rieder
- first_name: Emilio
full_name: Romano-Díaz, Emilio
last_name: Romano-Díaz
- first_name: Gautham
full_name: Sabhahit, Gautham
last_name: Sabhahit
- first_name: Andreas A. C.
full_name: Sander, Andreas A. C.
last_name: Sander
- first_name: Rafia
full_name: Sarwar, Rafia
last_name: Sarwar
- first_name: Hanno
full_name: Stinshoff, Hanno
last_name: Stinshoff
- first_name: Mitchel
full_name: Stoop, Mitchel
last_name: Stoop
- first_name: Dorottya
full_name: Szécsi, Dorottya
last_name: Szécsi
- first_name: Maxime
full_name: Trebitsch, Maxime
last_name: Trebitsch
- first_name: Jorick S.
full_name: Vink, Jorick S.
last_name: Vink
- first_name: Ethan
full_name: Winch, Ethan
last_name: Winch
citation:
ama: 'Geen S, Agrawal P, Crowther PA, et al. Bringing stellar evolution and feedback
together: Summary of proposals from the Lorentz Center workshop. Publications
of the Astronomical Society of the Pacific. 2023;135(1044). doi:10.1088/1538-3873/acb6b5'
apa: 'Geen, S., Agrawal, P., Crowther, P. A., Keller, B. W., de Koter, A., Keszthelyi,
Z., … Winch, E. (2023). Bringing stellar evolution and feedback together: Summary
of proposals from the Lorentz Center workshop. Publications of the Astronomical
Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/acb6b5'
chicago: 'Geen, Sam, Poojan Agrawal, Paul A. Crowther, B. W. Keller, Alex de Koter,
Zsolt Keszthelyi, Freeke van de Voort, et al. “Bringing Stellar Evolution and
Feedback Together: Summary of Proposals from the Lorentz Center Workshop.” Publications
of the Astronomical Society of the Pacific. IOP Publishing, 2023. https://doi.org/10.1088/1538-3873/acb6b5.'
ieee: 'S. Geen et al., “Bringing stellar evolution and feedback together:
Summary of proposals from the Lorentz Center workshop,” Publications of the
Astronomical Society of the Pacific, vol. 135, no. 1044. IOP Publishing, 2023.'
ista: 'Geen S, Agrawal P, Crowther PA, Keller BW, de Koter A, Keszthelyi Z, van
de Voort F, Ali AA, Backs F, Bonne L, Brugaletta V, Derkink A, Ekström S, Fichtner
YA, Grassitelli L, Götberg YLL, Higgins ER, Laplace E, You Liow K, Lorenzo M,
McLeod AF, Meynet G, Newsome M, André Oliva G, Ramachandran V, Rey MP, Rieder
S, Romano-Díaz E, Sabhahit G, Sander AAC, Sarwar R, Stinshoff H, Stoop M, Szécsi
D, Trebitsch M, Vink JS, Winch E. 2023. Bringing stellar evolution and feedback
together: Summary of proposals from the Lorentz Center workshop. Publications
of the Astronomical Society of the Pacific. 135(1044), 021001.'
mla: 'Geen, Sam, et al. “Bringing Stellar Evolution and Feedback Together: Summary
of Proposals from the Lorentz Center Workshop.” Publications of the Astronomical
Society of the Pacific, vol. 135, no. 1044, 021001, IOP Publishing, 2023,
doi:10.1088/1538-3873/acb6b5.'
short: S. Geen, P. Agrawal, P.A. Crowther, B.W. Keller, A. de Koter, Z. Keszthelyi,
F. van de Voort, A.A. Ali, F. Backs, L. Bonne, V. Brugaletta, A. Derkink, S. Ekström,
Y.A. Fichtner, L. Grassitelli, Y.L.L. Götberg, E.R. Higgins, E. Laplace, K. You
Liow, M. Lorenzo, A.F. McLeod, G. Meynet, M. Newsome, G. André Oliva, V. Ramachandran,
M.P. Rey, S. Rieder, E. Romano-Díaz, G. Sabhahit, A.A.C. Sander, R. Sarwar, H.
Stinshoff, M. Stoop, D. Szécsi, M. Trebitsch, J.S. Vink, E. Winch, Publications
of the Astronomical Society of the Pacific 135 (2023).
date_created: 2023-08-03T10:09:57Z
date_published: 2023-03-09T00:00:00Z
date_updated: 2023-08-21T12:09:14Z
day: '09'
doi: 10.1088/1538-3873/acb6b5
extern: '1'
external_id:
arxiv:
- '2301.13611'
intvolume: ' 135'
issue: '1044'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1538-3873/acb6b5
month: '03'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
eissn:
- 1538-3873
issn:
- 0004-6280
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bringing stellar evolution and feedback together: Summary of proposals from
the Lorentz Center workshop'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2023'
...
---
_id: '14104'
abstract:
- lang: eng
text: 'Thorne–Żytkow objects (TŻO) are potential end products of the merger of a
neutron star with a non-degenerate star. In this work, we have computed the first
grid of evolutionary models of TŻOs with the MESA stellar evolution code. With
these models, we predict several observational properties of TŻOs, including their
surface temperatures and luminosities, pulsation periods, and nucleosynthetic
products. We expand the range of possible TŻO solutions to cover 3.45≲log(Teff/K)≲3.65
and 4.85≲log(L/L⊙)≲5.5. Due to the much higher densities our TŻOs reach compared
to previous models, if TŻOs form we expect them to be stable over a larger mass
range than previously predicted, without exhibiting a gap in their mass distribution.
Using the GYRE stellar pulsation code we show that TŻOs should have fundamental
pulsation periods of 1000–2000 d, and period ratios of ≈0.2–0.3. Models computed
with a large 399 isotope fully coupled nuclear network show a nucleosynthetic
signal that is different to previously predicted. We propose a new nucleosynthetic
signal to determine a star’s status as a TŻO: the isotopologues 44TiO2 and 44TiO,
which will have a shift in their spectral features as compared to stable titanium-containing
molecules. We find that in the local Universe (∼SMC metallicities and above) TŻOs
show little heavy metal enrichment, potentially explaining the difficulty in finding
TŻOs to-date.'
article_processing_charge: No
article_type: original
author:
- first_name: R
full_name: Farmer, R
last_name: Farmer
- first_name: M
full_name: Renzo, M
last_name: Renzo
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: E
full_name: Bellinger, E
last_name: Bellinger
- first_name: S
full_name: Justham, S
last_name: Justham
- first_name: S E
full_name: de Mink, S E
last_name: de Mink
citation:
ama: Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. Observational
predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical
Society. 2023;524(2):1692-1709. doi:10.1093/mnras/stad1977
apa: Farmer, R., Renzo, M., Götberg, Y. L. L., Bellinger, E., Justham, S., &
de Mink, S. E. (2023). Observational predictions for Thorne–Żytkow objects. Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad1977
chicago: Farmer, R, M Renzo, Ylva Louise Linsdotter Götberg, E Bellinger, S Justham,
and S E de Mink. “Observational Predictions for Thorne–Żytkow Objects.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2023.
https://doi.org/10.1093/mnras/stad1977.
ieee: R. Farmer, M. Renzo, Y. L. L. Götberg, E. Bellinger, S. Justham, and S. E.
de Mink, “Observational predictions for Thorne–Żytkow objects,” Monthly Notices
of the Royal Astronomical Society, vol. 524, no. 2. Oxford University Press,
pp. 1692–1709, 2023.
ista: Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. 2023.
Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal
Astronomical Society. 524(2), 1692–1709.
mla: Farmer, R., et al. “Observational Predictions for Thorne–Żytkow Objects.” Monthly
Notices of the Royal Astronomical Society, vol. 524, no. 2, Oxford University
Press, 2023, pp. 1692–709, doi:10.1093/mnras/stad1977.
short: R. Farmer, M. Renzo, Y.L.L. Götberg, E. Bellinger, S. Justham, S.E. de Mink,
Monthly Notices of the Royal Astronomical Society 524 (2023) 1692–1709.
date_created: 2023-08-21T10:13:56Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-21T12:12:48Z
day: '01'
doi: 10.1093/mnras/stad1977
extern: '1'
external_id:
arxiv:
- '2305.07337'
intvolume: ' 524'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2305.07337
month: '09'
oa: 1
oa_version: Preprint
page: 1692-1709
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observational predictions for Thorne–Żytkow objects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 524
year: '2023'
...
---
_id: '13989'
abstract:
- lang: eng
text: Characterizing and controlling entanglement in quantum materials is crucial
for the development of next-generation quantum technologies. However, defining
a quantifiable figure of merit for entanglement in macroscopic solids is theoretically
and experimentally challenging. At equilibrium the presence of entanglement can
be diagnosed by extracting entanglement witnesses from spectroscopic observables
and a nonequilibrium extension of this method could lead to the discovery of novel
dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent
quantum Fisher information and entanglement depth of transient states of quantum
materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled
extended Hubbard model as an example, we benchmark the efficiency of this approach
and predict a light-enhanced many-body entanglement due to the proximity to a
phase boundary. Our work sets the stage for experimentally witnessing and controlling
entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.
article_number: '3512'
article_processing_charge: No
article_type: original
author:
- first_name: Jordyn
full_name: Hales, Jordyn
last_name: Hales
- first_name: Utkarsh
full_name: Bajpai, Utkarsh
last_name: Bajpai
- first_name: Tongtong
full_name: Liu, Tongtong
last_name: Liu
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Mingda
full_name: Li, Mingda
last_name: Li
- first_name: Matteo
full_name: Mitrano, Matteo
last_name: Mitrano
- first_name: Yao
full_name: Wang, Yao
last_name: Wang
citation:
ama: Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using
time-resolved resonant inelastic X-ray scattering. Nature Communications.
2023;14. doi:10.1038/s41467-023-38540-3
apa: Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &
Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant
inelastic X-ray scattering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38540-3
chicago: Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva,
Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement
Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38540-3.
ieee: J. Hales et al., “Witnessing light-driven entanglement using time-resolved
resonant inelastic X-ray scattering,” Nature Communications, vol. 14. Springer
Nature, 2023.
ista: Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing
light-driven entanglement using time-resolved resonant inelastic X-ray scattering.
Nature Communications. 14, 3512.
mla: Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved
Resonant Inelastic X-Ray Scattering.” Nature Communications, vol. 14, 3512,
Springer Nature, 2023, doi:10.1038/s41467-023-38540-3.
short: J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang,
Nature Communications 14 (2023).
date_created: 2023-08-09T13:06:59Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-08-22T06:50:04Z
day: '14'
doi: 10.1038/s41467-023-38540-3
extern: '1'
external_id:
arxiv:
- '2209.02283'
pmid:
- '37316515'
intvolume: ' 14'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-023-38540-3
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Witnessing light-driven entanglement using time-resolved resonant inelastic
X-ray scattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13990'
abstract:
- lang: eng
text: Many-body entanglement in condensed matter systems can be diagnosed from equilibrium
response functions through the use of entanglement witnesses and operator-specific
quantum bounds. Here, we investigate the applicability of this approach for detecting
entangled states in quantum systems driven out of equilibrium. We use a multipartite
entanglement witness, the quantum Fisher information, to study the dynamics of
a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb
interaction. Our results show that the quantum Fisher information is able to witness
distinct signatures of multipartite entanglement both near and far from equilibrium
that are robust against decoherence. We discuss implications of these findings
for probing entanglement in light-driven quantum materials with time-resolved
optical and x-ray scattering methods.
article_number: '106902'
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Mona H.
full_name: Kalthoff, Mona H.
last_name: Kalthoff
- first_name: Damian
full_name: Hofmann, Damian
last_name: Hofmann
- first_name: Martin
full_name: Claassen, Martin
last_name: Claassen
- first_name: Dante M.
full_name: Kennes, Dante M.
last_name: Kennes
- first_name: Michael A.
full_name: Sentef, Michael A.
last_name: Sentef
- first_name: Matteo
full_name: Mitrano, Matteo
last_name: Mitrano
citation:
ama: Baykusheva DR, Kalthoff MH, Hofmann D, et al. Witnessing nonequilibrium entanglement
dynamics in a strongly correlated fermionic chain. Physical Review Letters.
2023;130(10). doi:10.1103/physrevlett.130.106902
apa: Baykusheva, D. R., Kalthoff, M. H., Hofmann, D., Claassen, M., Kennes, D. M.,
Sentef, M. A., & Mitrano, M. (2023). Witnessing nonequilibrium entanglement
dynamics in a strongly correlated fermionic chain. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/physrevlett.130.106902
chicago: Baykusheva, Denitsa Rangelova, Mona H. Kalthoff, Damian Hofmann, Martin
Claassen, Dante M. Kennes, Michael A. Sentef, and Matteo Mitrano. “Witnessing
Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.”
Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106902.
ieee: D. R. Baykusheva et al., “Witnessing nonequilibrium entanglement dynamics
in a strongly correlated fermionic chain,” Physical Review Letters, vol.
130, no. 10. American Physical Society, 2023.
ista: Baykusheva DR, Kalthoff MH, Hofmann D, Claassen M, Kennes DM, Sentef MA, Mitrano
M. 2023. Witnessing nonequilibrium entanglement dynamics in a strongly correlated
fermionic chain. Physical Review Letters. 130(10), 106902.
mla: Baykusheva, Denitsa Rangelova, et al. “Witnessing Nonequilibrium Entanglement
Dynamics in a Strongly Correlated Fermionic Chain.” Physical Review Letters,
vol. 130, no. 10, 106902, American Physical Society, 2023, doi:10.1103/physrevlett.130.106902.
short: D.R. Baykusheva, M.H. Kalthoff, D. Hofmann, M. Claassen, D.M. Kennes, M.A.
Sentef, M. Mitrano, Physical Review Letters 130 (2023).
date_created: 2023-08-09T13:07:24Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-22T07:18:01Z
day: '10'
doi: 10.1103/physrevlett.130.106902
extern: '1'
external_id:
arxiv:
- '2209.02081'
pmid:
- '36962013'
intvolume: ' 130'
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.02081
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic
chain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 130
year: '2023'
...
---
_id: '12697'
abstract:
- lang: eng
text: Models for same-material contact electrification in granular media often rely
on a local charge-driving parameter whose spatial variations lead to a stochastic
origin for charge exchange. Measuring the charge transfer from individual granular
spheres after contacts with substrates of the same material, we find instead a
“global” charging behavior, coherent over the sample’s whole surface. Cleaning
and baking samples fully resets charging magnitude and direction, which indicates
the underlying global parameter is not intrinsic to the material, but acquired
from its history. Charging behavior is randomly and irreversibly affected by changes
in relative humidity, hinting at a mechanism where adsorbates, in particular,
water, are fundamental to the charge-transfer process.
acknowledgement: "We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti
for helpful discussions. This project has received funding from the European Research
Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant
Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation
program."
article_number: '098202'
article_processing_charge: No
article_type: original
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism
driven by sample history for contact electrification in granular media. Physical
Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202
apa: Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics
reveal a global mechanism driven by sample history for contact electrification
in granular media. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.130.098202
chicago: Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters. American Physical Society,
2023. https://doi.org/10.1103/physrevlett.130.098202.
ieee: G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal
a global mechanism driven by sample history for contact electrification in granular
media,” Physical Review Letters, vol. 130, no. 9. American Physical Society,
2023.
ista: Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global
mechanism driven by sample history for contact electrification in granular media.
Physical Review Letters. 130(9), 098202.
mla: Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American
Physical Society, 2023, doi:10.1103/physrevlett.130.098202.
short: G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).
date_created: 2023-02-28T12:14:46Z
date_published: 2023-03-03T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '03'
ddc:
- '530'
- '537'
department:
- _id: ScWa
doi: 10.1103/physrevlett.130.098202
ec_funded: 1
external_id:
arxiv:
- '2211.02488'
isi:
- '000946178200008'
file:
- access_level: open_access
checksum: c4f2f6eea0408811f8f4898e15890355
content_type: application/pdf
creator: ggrosjea
date_created: 2023-02-28T12:20:27Z
date_updated: 2023-02-28T12:20:27Z
file_id: '12698'
file_name: Main_Preprint.pdf
file_size: 2301864
relation: main_file
success: 1
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checksum: 6af6ed6c97a977f923de4162294b43c4
content_type: application/pdf
creator: ggrosjea
date_created: 2023-02-28T12:20:55Z
date_updated: 2023-02-28T12:20:55Z
file_id: '12699'
file_name: Suppl_info.pdf
file_size: 1138625
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success: 1
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date_updated: 2023-02-28T12:37:54Z
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file_size: 793449
relation: main_file
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creator: ggrosjea
date_created: 2023-02-28T12:37:54Z
date_updated: 2023-02-28T12:37:54Z
file_id: '12701'
file_name: Suppl_vid2.mp4
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relation: main_file
success: 1
file_date_updated: 2023-02-28T12:37:54Z
has_accepted_license: '1'
intvolume: ' 130'
isi: 1
issue: '9'
keyword:
- General Physics
- Electrostatics
- Triboelectricity
- Soft Matter
- Acoustic Levitation
- Granular Materials
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2211.02488
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '8101'
relation: research_paper
status: public
status: public
title: Single-collision statistics reveal a global mechanism driven by sample history
for contact electrification in granular media
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '14103'
abstract:
- lang: eng
text: Observations of individual massive stars, super-luminous supernovae, gamma-ray
bursts, and gravitational wave events involving spectacular black hole mergers
indicate that the low-metallicity Universe is fundamentally different from our
own Galaxy. Many transient phenomena will remain enigmatic until we achieve a
firm understanding of the physics and evolution of massive stars at low metallicity
(Z). The Hubble Space Telescope has devoted 500 orbits to observing ∼250 massive
stars at low Z in the ultraviolet (UV) with the COS and STIS spectrographs under
the ULLYSES programme. The complementary X-Shooting ULLYSES (XShootU) project
provides an enhanced legacy value with high-quality optical and near-infrared
spectra obtained with the wide-wavelength coverage X-shooter spectrograph at ESO’s
Very Large Telescope. We present an overview of the XShootU project, showing that
combining ULLYSES UV and XShootU optical spectra is critical for the uniform determination
of stellar parameters such as effective temperature, surface gravity, luminosity,
and abundances, as well as wind properties such as mass-loss rates as a function
of Z. As uncertainties in stellar and wind parameters percolate into many adjacent
areas of astrophysics, the data and modelling of the XShootU project is expected
to be a game changer for our physical understanding of massive stars at low Z.
To be able to confidently interpret James Webb Space Telescope spectra of the
first stellar generations, the individual spectra of low-Z stars need to be understood,
which is exactly where XShootU can deliver.
article_number: A154
article_processing_charge: No
article_type: original
author:
- first_name: Jorick S.
full_name: Vink, Jorick S.
last_name: Vink
- first_name: A.
full_name: Mehner, A.
last_name: Mehner
- first_name: P. A.
full_name: Crowther, P. A.
last_name: Crowther
- first_name: A.
full_name: Fullerton, A.
last_name: Fullerton
- first_name: M.
full_name: Garcia, M.
last_name: Garcia
- first_name: F.
full_name: Martins, F.
last_name: Martins
- first_name: N.
full_name: Morrell, N.
last_name: Morrell
- first_name: L. M.
full_name: Oskinova, L. M.
last_name: Oskinova
- first_name: N.
full_name: St-Louis, N.
last_name: St-Louis
- first_name: A.
full_name: ud-Doula, A.
last_name: ud-Doula
- first_name: A. A. C.
full_name: Sander, A. A. C.
last_name: Sander
- first_name: H.
full_name: Sana, H.
last_name: Sana
- first_name: J.-C.
full_name: Bouret, J.-C.
last_name: Bouret
- first_name: B.
full_name: Kubátová, B.
last_name: Kubátová
- first_name: P.
full_name: Marchant, P.
last_name: Marchant
- first_name: L. P.
full_name: Martins, L. P.
last_name: Martins
- first_name: A.
full_name: Wofford, A.
last_name: Wofford
- first_name: J. Th.
full_name: van Loon, J. Th.
last_name: van Loon
- first_name: O.
full_name: Grace Telford, O.
last_name: Grace Telford
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: D. M.
full_name: Bowman, D. M.
last_name: Bowman
- first_name: C.
full_name: Erba, C.
last_name: Erba
- first_name: V. M.
full_name: Kalari, V. M.
last_name: Kalari
- first_name: M.
full_name: Abdul-Masih, M.
last_name: Abdul-Masih
- first_name: T.
full_name: Alkousa, T.
last_name: Alkousa
- first_name: F.
full_name: Backs, F.
last_name: Backs
- first_name: C. L.
full_name: Barbosa, C. L.
last_name: Barbosa
- first_name: S. R.
full_name: Berlanas, S. R.
last_name: Berlanas
- first_name: M.
full_name: Bernini-Peron, M.
last_name: Bernini-Peron
- first_name: J. M.
full_name: Bestenlehner, J. M.
last_name: Bestenlehner
- first_name: R.
full_name: Blomme, R.
last_name: Blomme
- first_name: J.
full_name: Bodensteiner, J.
last_name: Bodensteiner
- first_name: S. A.
full_name: Brands, S. A.
last_name: Brands
- first_name: C. J.
full_name: Evans, C. J.
last_name: Evans
- first_name: A.
full_name: David-Uraz, A.
last_name: David-Uraz
- first_name: F. A.
full_name: Driessen, F. A.
last_name: Driessen
- first_name: K.
full_name: Dsilva, K.
last_name: Dsilva
- first_name: S.
full_name: Geen, S.
last_name: Geen
- first_name: V. M. A.
full_name: Gómez-González, V. M. A.
last_name: Gómez-González
- first_name: L.
full_name: Grassitelli, L.
last_name: Grassitelli
- first_name: W.-R.
full_name: Hamann, W.-R.
last_name: Hamann
- first_name: C.
full_name: Hawcroft, C.
last_name: Hawcroft
- first_name: A.
full_name: Herrero, A.
last_name: Herrero
- first_name: E. R.
full_name: Higgins, E. R.
last_name: Higgins
- first_name: D.
full_name: John Hillier, D.
last_name: John Hillier
- first_name: R.
full_name: Ignace, R.
last_name: Ignace
- first_name: A. G.
full_name: Istrate, A. G.
last_name: Istrate
- first_name: L.
full_name: Kaper, L.
last_name: Kaper
- first_name: N. D.
full_name: Kee, N. D.
last_name: Kee
- first_name: C.
full_name: Kehrig, C.
last_name: Kehrig
- first_name: Z.
full_name: Keszthelyi, Z.
last_name: Keszthelyi
- first_name: J.
full_name: Klencki, J.
last_name: Klencki
- first_name: A.
full_name: de Koter, A.
last_name: de Koter
- first_name: R.
full_name: Kuiper, R.
last_name: Kuiper
- first_name: E.
full_name: Laplace, E.
last_name: Laplace
- first_name: C. J. K.
full_name: Larkin, C. J. K.
last_name: Larkin
- first_name: R. R.
full_name: Lefever, R. R.
last_name: Lefever
- first_name: C.
full_name: Leitherer, C.
last_name: Leitherer
- first_name: D. J.
full_name: Lennon, D. J.
last_name: Lennon
- first_name: L.
full_name: Mahy, L.
last_name: Mahy
- first_name: J.
full_name: Maíz Apellániz, J.
last_name: Maíz Apellániz
- first_name: G.
full_name: Maravelias, G.
last_name: Maravelias
- first_name: W.
full_name: Marcolino, W.
last_name: Marcolino
- first_name: A. F.
full_name: McLeod, A. F.
last_name: McLeod
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: F.
full_name: Najarro, F.
last_name: Najarro
- first_name: M. S.
full_name: Oey, M. S.
last_name: Oey
- first_name: T. N.
full_name: Parsons, T. N.
last_name: Parsons
- first_name: D.
full_name: Pauli, D.
last_name: Pauli
- first_name: M. G.
full_name: Pedersen, M. G.
last_name: Pedersen
- first_name: R. K.
full_name: Prinja, R. K.
last_name: Prinja
- first_name: V.
full_name: Ramachandran, V.
last_name: Ramachandran
- first_name: M. C.
full_name: Ramírez-Tannus, M. C.
last_name: Ramírez-Tannus
- first_name: G. N.
full_name: Sabhahit, G. N.
last_name: Sabhahit
- first_name: A.
full_name: Schootemeijer, A.
last_name: Schootemeijer
- first_name: S.
full_name: Reyero Serantes, S.
last_name: Reyero Serantes
- first_name: T.
full_name: Shenar, T.
last_name: Shenar
- first_name: G. S.
full_name: Stringfellow, G. S.
last_name: Stringfellow
- first_name: N.
full_name: Sudnik, N.
last_name: Sudnik
- first_name: F.
full_name: Tramper, F.
last_name: Tramper
- first_name: L.
full_name: Wang, L.
last_name: Wang
citation:
ama: 'Vink JS, Mehner A, Crowther PA, et al. X-shooting ULLYSES: Massive stars at
low metallicity. I. Project description. Astronomy & Astrophysics.
2023;675. doi:10.1051/0004-6361/202245650'
apa: 'Vink, J. S., Mehner, A., Crowther, P. A., Fullerton, A., Garcia, M., Martins,
F., … Wang, L. (2023). X-shooting ULLYSES: Massive stars at low metallicity. I.
Project description. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202245650'
chicago: 'Vink, Jorick S., A. Mehner, P. A. Crowther, A. Fullerton, M. Garcia, F.
Martins, N. Morrell, et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity.
I. Project Description.” Astronomy & Astrophysics. EDP Sciences, 2023.
https://doi.org/10.1051/0004-6361/202245650.'
ieee: 'J. S. Vink et al., “X-shooting ULLYSES: Massive stars at low metallicity.
I. Project description,” Astronomy & Astrophysics, vol. 675. EDP Sciences,
2023.'
ista: 'Vink JS, Mehner A, Crowther PA, Fullerton A, Garcia M, Martins F, Morrell
N, Oskinova LM, St-Louis N, ud-Doula A, Sander AAC, Sana H, Bouret J-C, Kubátová
B, Marchant P, Martins LP, Wofford A, van Loon JT, Grace Telford O, Götberg YLL,
Bowman DM, Erba C, Kalari VM, Abdul-Masih M, Alkousa T, Backs F, Barbosa CL, Berlanas
SR, Bernini-Peron M, Bestenlehner JM, Blomme R, Bodensteiner J, Brands SA, Evans
CJ, David-Uraz A, Driessen FA, Dsilva K, Geen S, Gómez-González VMA, Grassitelli
L, Hamann W-R, Hawcroft C, Herrero A, Higgins ER, John Hillier D, Ignace R, Istrate
AG, Kaper L, Kee ND, Kehrig C, Keszthelyi Z, Klencki J, de Koter A, Kuiper R,
Laplace E, Larkin CJK, Lefever RR, Leitherer C, Lennon DJ, Mahy L, Maíz Apellániz
J, Maravelias G, Marcolino W, McLeod AF, de Mink SE, Najarro F, Oey MS, Parsons
TN, Pauli D, Pedersen MG, Prinja RK, Ramachandran V, Ramírez-Tannus MC, Sabhahit
GN, Schootemeijer A, Reyero Serantes S, Shenar T, Stringfellow GS, Sudnik N, Tramper
F, Wang L. 2023. X-shooting ULLYSES: Massive stars at low metallicity. I. Project
description. Astronomy & Astrophysics. 675, A154.'
mla: 'Vink, Jorick S., et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity.
I. Project Description.” Astronomy & Astrophysics, vol. 675, A154,
EDP Sciences, 2023, doi:10.1051/0004-6361/202245650.'
short: J.S. Vink, A. Mehner, P.A. Crowther, A. Fullerton, M. Garcia, F. Martins,
N. Morrell, L.M. Oskinova, N. St-Louis, A. ud-Doula, A.A.C. Sander, H. Sana, J.-C.
Bouret, B. Kubátová, P. Marchant, L.P. Martins, A. Wofford, J.T. van Loon, O.
Grace Telford, Y.L.L. Götberg, D.M. Bowman, C. Erba, V.M. Kalari, M. Abdul-Masih,
T. Alkousa, F. Backs, C.L. Barbosa, S.R. Berlanas, M. Bernini-Peron, J.M. Bestenlehner,
R. Blomme, J. Bodensteiner, S.A. Brands, C.J. Evans, A. David-Uraz, F.A. Driessen,
K. Dsilva, S. Geen, V.M.A. Gómez-González, L. Grassitelli, W.-R. Hamann, C. Hawcroft,
A. Herrero, E.R. Higgins, D. John Hillier, R. Ignace, A.G. Istrate, L. Kaper,
N.D. Kee, C. Kehrig, Z. Keszthelyi, J. Klencki, A. de Koter, R. Kuiper, E. Laplace,
C.J.K. Larkin, R.R. Lefever, C. Leitherer, D.J. Lennon, L. Mahy, J. Maíz Apellániz,
G. Maravelias, W. Marcolino, A.F. McLeod, S.E. de Mink, F. Najarro, M.S. Oey,
T.N. Parsons, D. Pauli, M.G. Pedersen, R.K. Prinja, V. Ramachandran, M.C. Ramírez-Tannus,
G.N. Sabhahit, A. Schootemeijer, S. Reyero Serantes, T. Shenar, G.S. Stringfellow,
N. Sudnik, F. Tramper, L. Wang, Astronomy & Astrophysics 675 (2023).
date_created: 2023-08-21T10:12:35Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-22T11:01:07Z
day: '01'
doi: 10.1051/0004-6361/202245650
extern: '1'
external_id:
arxiv:
- '2305.06376'
intvolume: ' 675'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/202245650
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'X-shooting ULLYSES: Massive stars at low metallicity. I. Project description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 675
year: '2023'
...
---
_id: '13175'
abstract:
- lang: eng
text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13175
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:13175.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-06-30T08:07:43Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-24T11:16:35Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:13175
ec_funded: 1
file:
- access_level: open_access
checksum: 7d03f1a5a5258ee43dfc3323dea4e08f
content_type: application/pdf
creator: cchlebak
date_created: 2023-06-30T08:17:25Z
date_updated: 2023-06-30T08:17:25Z
file_id: '13176'
file_name: thesis_pdfa.pdf
file_size: 18688376
relation: main_file
success: 1
- access_level: closed
checksum: c3b45317ae58e0527533f98c202d81b7
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-07-06T11:35:15Z
date_updated: 2023-07-06T11:35:15Z
file_id: '13196'
file_name: thesis.zip
file_size: 37847025
relation: source_file
file_date_updated: 2023-07-06T11:35:15Z
has_accepted_license: '1'
keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '202'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12900'
relation: old_edition
status: public
- id: '10924'
relation: part_of_dissertation
status: public
- id: '9114'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14242'
abstract:
- lang: eng
text: We study the problem of training and certifying adversarially robust quantized
neural networks (QNNs). Quantization is a technique for making neural networks
more efficient by running them using low-bit integer arithmetic and is therefore
commonly adopted in industry. Recent work has shown that floating-point neural
networks that have been verified to be robust can become vulnerable to adversarial
attacks after quantization, and certification of the quantized representation
is necessary to guarantee robustness. In this work, we present quantization-aware
interval bound propagation (QA-IBP), a novel method for training robust QNNs.
Inspired by advances in robust learning of non-quantized networks, our training
algorithm computes the gradient of an abstract representation of the actual network.
Unlike existing approaches, our method can handle the discrete semantics of QNNs.
Based on QA-IBP, we also develop a complete verification procedure for verifying
the adversarial robustness of QNNs, which is guaranteed to terminate and produce
a correct answer. Compared to existing approaches, the key advantage of our verification
procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate
experimentally that our approach significantly outperforms existing methods and
establish the new state-of-the-art for training and certifying the robustness
of QNNs.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research
was sponsored by the United\r\nStates Air Force Research Laboratory and the United
States Air Force Artificial Intelligence Accelerator and was accomplished under
Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained
in this document are those of the authors and should not be interpreted as representing
the official policies, either expressed or implied,\r\nof the United States Air
Force or the U.S. Government. The U.S. Government is authorized to reproduce and
distribute reprints for Government purposes notwithstanding any copyright\r\nnotation
herein. The research was also funded in part by the AI2050 program at Schmidt Futures
(Grant G-22-63172) and Capgemini SE."
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973.
doi:10.1609/aaai.v37i12.26747'
apa: 'Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D.
(2023). Quantization-aware interval bound propagation for training certifiably
robust quantized neural networks. In Proceedings of the 37th AAAI Conference
on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747'
chicago: Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger,
and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably
Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 37:14964–73. Association for the Advancement of
Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.
ieee: M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks,”
in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.
ista: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference
on Artificial Intelligence vol. 37, 14964–14973.'
mla: Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for
Training Certifiably Robust Quantized Neural Networks.” Proceedings of the
37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association
for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.
short: M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 14964–14973.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:17Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2023-09-05T07:06:14Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i12.26747
ec_funded: 1
external_id:
arxiv:
- '2211.16187'
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.16187
month: '06'
oa: 1
oa_version: Preprint
page: 14964-14973
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantization-aware interval bound propagation for training certifiably robust
quantized neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14243'
abstract:
- lang: eng
text: 'Two-player zero-sum "graph games" are central in logic, verification, and
multi-agent systems. The game proceeds by placing a token on a vertex of a graph,
and allowing the players to move it to produce an infinite path, which determines
the winner or payoff of the game. Traditionally, the players alternate turns in
moving the token. In "bidding games", however, the players have budgets and in
each turn, an auction (bidding) determines which player moves the token. So far,
bidding games have only been studied as full-information games. In this work we
initiate the study of partial-information bidding games: we study bidding games
in which a player''s initial budget is drawn from a known probability distribution.
We show that while for some bidding mechanisms and objectives, it is straightforward
to adapt the results from the full-information setting to the partial-information
setting, for others, the analysis is significantly more challenging, requires
new techniques, and gives rise to interesting results. Specifically, we study
games with "mean-payoff" objectives in combination with "poorman" bidding. We
construct optimal strategies for a partially-informed player who plays against
a fully-informed adversary. We show that, somewhat surprisingly, the "value" under
pure strategies does not necessarily exist in such games.'
acknowledgement: This research was supported in part by ISF grant no.1679/21, by the
ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable
budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679'
apa: Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with
partially-observable budgets. In Proceedings of the 37th AAAI Conference on
Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States.
https://doi.org/10.1609/aaai.v37i5.25679
chicago: Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with
Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on
Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.
ieee: G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable
budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.
ista: 'Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable
budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI:
Conference on Artificial Intelligence vol. 37, 5464–5471.'
mla: Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.”
Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol.
37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.
short: G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 2023, pp. 5464–5471.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:18Z
date_published: 2023-06-27T00:00:00Z
date_updated: 2023-09-05T08:37:00Z
day: '27'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i5.25679
ec_funded: 1
external_id:
arxiv:
- '2211.13626'
intvolume: ' 37'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1609/aaai.v37i5.25679
month: '06'
oa: 1
oa_version: Published Version
page: 5464-5471
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bidding graph games with partially-observable budgets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14241'
abstract:
- lang: eng
text: We present a technique to optimize the reflectivity of a surface while preserving
its overall shape. The naïve optimization of the mesh vertices using the gradients
of reflectivity simulations results in undesirable distortion. In contrast, our
robust formulation optimizes the surface normal as an independent variable that
bridges the reflectivity term with differential rendering, and the regularization
term with as-rigid-as-possible elastic energy. We further adaptively subdivide
the input mesh to improve the convergence. Consequently, our method can minimize
the retroreflectivity of a wide range of input shapes, resulting in sharply creased
shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by
changing the reward for the direction of the outgoing light directions, our method
can be applied to other reflectivity design tasks, such as the optimization of
architectural walls to concentrate light in a specific region. We have tested
the proposed method using light-transport simulations and real-world 3D-printed
objects.
acknowledgement: "The authors would like to thank Yuki Koyama and Takeo Igarashi for
early discussions, and Yuta Yaguchi for support in 3D printing. This research is
partially supported by the Israel Science Foundation grant number 1390/19.\r\n"
article_number: '20'
article_processing_charge: No
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization
as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association
for Computing Machinery; 2023. doi:10.1145/3588432.3591542'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper:
Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference
Proceedings. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3588432.3591542'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth
Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023
Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity
optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings,
Los Angeles, CA, United States, 2023.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity
optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH:
Computer Graphics and Interactive Techniques Conference, 20.'
mla: 'Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface
Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for
Computing Machinery, 2023, doi:10.1145/3588432.3591542.'
short: K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference
Proceedings, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-08-27T22:01:17Z
date_published: 2023-07-23T00:00:00Z
date_updated: 2023-09-05T07:22:03Z
day: '23'
department:
- _id: BeBi
doi: 10.1145/3588432.3591542
external_id:
arxiv:
- '2305.05944'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.05944
month: '07'
oa: 1
oa_version: Preprint
publication: SIGGRAPH 2023 Conference Proceedings
publication_identifier:
isbn:
- '9798400701597'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Stealth shaper: Reflectivity optimization as surface stylization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13310'
abstract:
- lang: eng
text: Machine-learned systems are in widespread use for making decisions about humans,
and it is important that they are fair, i.e., not biased against individuals based
on sensitive attributes. We present runtime verification of algorithmic fairness
for systems whose models are unknown, but are assumed to have a Markov chain structure.
We introduce a specification language that can model many common algorithmic fairness
properties, such as demographic parity, equal opportunity, and social burden.
We build monitors that observe a long sequence of events as generated by a given
system, and output, after each observation, a quantitative estimate of how fair
or biased the system was on that run until that point in time. The estimate is
proven to be correct modulo a variable error bound and a given confidence level,
where the error bound gets tighter as the observed sequence gets longer. Our monitors
are of two types, and use, respectively, frequentist and Bayesian statistical
inference techniques. While the frequentist monitors compute estimates that are
objectively correct with respect to the ground truth, the Bayesian monitors compute
estimates that are correct subject to a given prior belief about the system’s
model. Using a prototype implementation, we show how we can monitor if a bank
is fair in giving loans to applicants from different social backgrounds, and if
a college is fair in admitting students while maintaining a reasonable financial
burden on the society. Although they exhibit different theoretical complexities
in certain cases, in our experiments, both frequentist and Bayesian monitors took
less than a millisecond to update their verdicts after each observation.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG101020093.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mahyar
full_name: Karimi, Mahyar
id: f1dedef5-2f78-11ee-989a-c4c97bccf506
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness.
In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382.
doi:10.1007/978-3-031-37703-7_17'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring
algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382).
Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17'
chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.
ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic
fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965,
pp. 358–382.
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic
fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13965, 358–382.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer
Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.
short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 358–382.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-07-25T18:32:40Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-05T15:14:00Z
day: '18'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-37703-7_17
ec_funded: 1
external_id:
arxiv:
- '2305.15979'
file:
- access_level: open_access
checksum: ccaf94bf7d658ba012c016e11869b54c
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:11:20Z
date_updated: 2023-07-31T08:11:20Z
file_id: '13327'
file_name: 2023_LNCS_CAV_HenzingerT.pdf
file_size: 647760
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:11:20Z
has_accepted_license: '1'
intvolume: ' 13965'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 358–382
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377037'
eissn:
- 1611-3349
isbn:
- '9783031377020'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Monitoring algorithmic fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13965
year: '2023'
...