---
_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
license: https://creativecommons.org/licenses/by/4.0/
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: '13237'
abstract:
- lang: eng
text: The formation of amyloid fibrils is a general class of protein self-assembly
behaviour, which is associated with both functional biology and the development
of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review,
we discuss how general physical concepts from the study of phase transitions can
be used to illuminate the fundamental mechanisms of amyloid self-assembly. We
summarize progress in the efforts to describe the essential biophysical features
of amyloid self-assembly as a nucleation-and-growth process and discuss how master
equation approaches can reveal the key molecular pathways underlying this process,
including the role of secondary nucleation. Additionally, we outline how non-classical
aspects of aggregate formation involving oligomers or biomolecular condensates
have emerged, inspiring developments in understanding, modelling and modulating
complex protein assembly pathways. Finally, we consider how these concepts can
be applied to kinetics-based drug discovery and therapeutic design to develop
treatments for protein aggregation diseases.
acknowledgement: The authors acknowledge support from the Institute for the Physics
of Living Systems, University College London (T.C.T.M.), the Swedish Research Council
(2015-00143) (S.L.), the European Research Council under the European Union’s Seventh
Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no.
337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the
Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C.
Flandoli for help with illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Daoyuan
full_name: Qian, Daoyuan
last_name: Qian
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid
formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397.
doi:10.1038/s42254-023-00598-9
apa: Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &
Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature
Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9
chicago: Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo,
Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.
ieee: T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P.
J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews
Physics, vol. 5. Springer Nature, pp. 379–397, 2023.
ista: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023.
Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.
mla: Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.
short: T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles,
Nature Reviews Physics 5 (2023) 379–397.
date_created: 2023-07-16T22:01:12Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:28:38Z
day: '01'
department:
- _id: AnSa
doi: 10.1038/s42254-023-00598-9
external_id:
isi:
- '001017539800001'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 379–397
publication: Nature Reviews Physics
publication_identifier:
eissn:
- 2522-5820
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Amyloid formation as a protein phase transition
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
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: '13235'
abstract:
- lang: eng
text: AgSbSe2 is a promising thermoelectric (TE) p-type material for applications
in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal
conductivities and high Seebeck coefficients, but its main limitation is moderate
electrical conductivity. Herein, we detail an efficient and scalable hot-injection
synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier
concentration and improve the electrical conductivity, these NCs are doped with
Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using
a reducing NaBH4 solution to displace the organic ligand and anneal the material
under a forming gas flow. The TE properties of the dense materials obtained from
the consolidation of the NCs using a hot pressing are then characterized. The
presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier
concentration and, consequently, the electrical conductivity. Opportunely, the
measured Seebeck coefficient varied within a small range upon Sn doping. The excellent
performance obtained when Sn2+ ions are prevented from oxidation is rationalized
by modeling the system. Calculated band structures disclosed that Sn doping induces
convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic
effective mass. The dramatically enhanced carrier transport leads to a maximized
power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon
scattering is significantly enhanced in the NC-based materials, yielding an ultralow
thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of
merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above
the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and
Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate
for medium-temperature TE applications.
acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation
of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project
of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges
financial support from the National Natural Science Foundation of China (Grant No.
22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful
for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229).
M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mingquan
full_name: Li, Mingquan
last_name: Li
- first_name: Shanhong
full_name: Wan, Shanhong
last_name: Wan
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Min
full_name: Hong, Min
last_name: Hong
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂:
Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934.
doi:10.1021/acsnano.3c03541'
apa: 'Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023).
Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541'
chicago: 'Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li,
Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band
Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano.
American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541.'
ieee: 'Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂:
Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American
Chemical Society, pp. 11923–11934, 2023.'
ista: 'Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot
A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance. ACS Nano. 17(12), 11923–11934.'
mla: 'Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward
High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical
Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.'
short: Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong,
A. Cabot, ACS Nano 17 (2023) 11923–11934.
date_created: 2023-07-16T22:01:11Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2023-08-02T06:29:55Z
day: '13'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c03541
external_id:
isi:
- '001008564800001'
pmid:
- '37310395'
intvolume: ' 17'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 11923–11934
pmid: 1
project:
- _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 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: 'Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
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: '12781'
abstract:
- lang: eng
text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory
chain consisting of several protein assemblies embedded into lipid membrane (complexes
I-V). Complex I is the first and the largest enzyme of the respiratory chain which
is essential for energy production. It couples the transfer of two electrons from
NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial
membrane. The coupling mechanism between electron transfer and proton translocation
is one of the biggest enigma in bioenergetics and structural biology. Even though
the enzyme has been studied for decades, only recent technological advances in
cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from
E.coli appears to be of special importance because it is a perfect model system
with a rich mutant library, however the structure of the entire complex was unknown.
In this thesis I have resolved structures of the minimal complex I version from
E. coli in different states including reduced, inhibited, under reaction turnover
and several others. Extensive structural analyses of these structures and comparison
to structures from other species allowed to derive general features of conformational
dynamics and propose a universal coupling mechanism. The mechanism is straightforward,
robust and consistent with decades of experimental data available for complex
I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I)
is a part of broad complex I superfamily and was studied as well in this thesis.
It plays an important role in cyclic electron transfer (CET), during which electrons
are cycled within PSI through ferredoxin and plastoquinone to generate proton
gradient without NADPH production. Here, I solved structure of NDH and revealed
additional state, which was not observed before. The novel “resting” state allowed
to propose the mechanism of CET regulation. Moreover, conformational dynamics
of NDH resembles one in complex I which suggest more broad universality of the
proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped
to interpret decades of experimental data for complex I and contributed to fundamental
mechanistic understanding of protein function.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
citation:
ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its
cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781
apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex
I and its cyanobacterial ortholog. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12781
chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12781.
ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and
its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.
ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I
and its cyanobacterial ortholog. Institute of Science and Technology Austria.
mla: Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12781.
short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and
Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-31T12:24:42Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2023-08-04T08:54:51Z
day: '23'
ddc:
- '570'
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LeSa
doi: 10.15479/at:ista:12781
ec_funded: 1
file:
- access_level: closed
checksum: 5ebb6345cb4119f93460c81310265a6d
content_type: application/pdf
creator: vkravchu
date_created: 2023-04-19T14:33:41Z
date_updated: 2023-04-19T14:33:41Z
embargo: 2024-04-20
embargo_to: local
file_id: '12852'
file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf
file_size: 6071553
relation: main_file
- access_level: closed
checksum: c12055c48411d030d2afa51de2166221
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: vkravchu
date_created: 2023-04-19T14:33:52Z
date_updated: 2023-04-20T07:02:59Z
embargo: 2024-04-20
embargo_to: local
file_id: '12853'
file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx
file_size: 19468766
relation: source_file
file_date_updated: 2023-04-20T07:02:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa_version: Published Version
page: '127'
project:
- _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E
grant_number: '25541'
name: 'Structural characterization of E. coli complex I: an important mechanistic
model'
- _id: 627abdeb-2b32-11ec-9570-ec31a97243d3
call_identifier: H2020
grant_number: '101020697'
name: Structure and mechanism of respiratory chain molecular machines
publication_identifier:
isbn:
- 978-3-99078-029-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12138'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Structural and mechanistic study of bacterial complex I and its cyanobacterial
ortholog
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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:
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creator: epeste
date_created: 2023-05-24T16:11:16Z
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language:
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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: '12964'
abstract:
- lang: eng
text: "Pattern formation is of great importance for its contribution across different
biological behaviours. During developmental processes for example, patterns of
chemical gradients are\r\nestablished to determine cell fate and complex tissue
patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns
are also seen in collectively migrating groups, for\r\ninstance traveling waves
of density emerging in moving animal flocks as well as collectively migrating
cells and tissues. To what extent these biological patterns arise spontaneously
through\r\nthe local interaction of individual constituents or are dictated by
higher level instructions is\r\nstill an open question however there is evidence
for the involvement of both types of process.\r\nWhere patterns arise spontaneously
there is a long standing interest in how far the interplay\r\nof mechanics, e.g.
force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling,
contributes to the behaviour. This is because many systems are able to both\r\nchemically
regulate mechanical force production and chemically sense mechanical deformation,\r\nforming
mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio
and/or temporal patterning.\r\nWe work with experimental collaborators to investigate
the possibility that this type of\r\ninteraction drives pattern formation in biological
systems at different scales. We focus first on\r\ntissue-level ERK-density waves
observed during the wound healing response across different\r\nsystems where many
previous studies have proposed that patterns depend on polarized cell\r\nmigration
and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical
and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence
for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween
ERK signaling and cell contraction. We perform further modeling and experiment\r\nto
study how this instability couples with polar cell migration in order to produce
a robust\r\nand efficient wound healing response. In a following chapter we implement
ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate
the interaction of\r\nERK-density patterning with different tissue rheologies
and find that the spatio-temporal\r\ndynamics are able to both locally and globally
fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter
we move towards lower spatial scales in the context of subcellular\r\npatterning
of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially
homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics
of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand
its activator). Experimental evidence supports an intrinsic chemical oscillator
which we\r\nencode in a reaction model and couple to a contractile active gel
description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations
and contractile spatial patterning which\r\nreproduce many features of the dynamics
seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological
perturbations to inhibit myosin contractility leaves the role of\r\ncontractile
instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof
reaction-diffusion instability."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
citation:
ama: Boocock DR. Mechanochemical pattern formation across biological scales. 2023.
doi:10.15479/at:ista:12964
apa: Boocock, D. R. (2023). Mechanochemical pattern formation across biological
scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964
chicago: Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological
Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.
ieee: D. R. Boocock, “Mechanochemical pattern formation across biological scales,”
Institute of Science and Technology Austria, 2023.
ista: Boocock DR. 2023. Mechanochemical pattern formation across biological scales.
Institute of Science and Technology Austria.
mla: Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.
short: D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales,
Institute of Science and Technology Austria, 2023.
date_created: 2023-05-15T14:52:36Z
date_published: 2023-05-17T00:00:00Z
date_updated: 2023-08-04T11:02:40Z
day: '17'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EdHa
doi: 10.15479/at:ista:12964
ec_funded: 1
file:
- access_level: closed
checksum: d51240675fc6dc0e3f5dc0c902695d3a
content_type: application/pdf
creator: dboocock
date_created: 2023-05-17T13:39:54Z
date_updated: 2023-05-19T07:04:25Z
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embargo_to: open_access
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file_name: thesis_boocock.pdf
file_size: 40414730
relation: main_file
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checksum: 581a2313ffeb40fe77e8a122a25a7795
content_type: application/zip
creator: dboocock
date_created: 2023-05-17T13:39:53Z
date_updated: 2023-05-17T14:35:13Z
file_id: '12989'
file_name: thesis_boocock.zip
file_size: 34338567
relation: source_file
file_date_updated: 2023-05-19T07:04:25Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '05'
oa_version: Published Version
page: '146'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-032-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8602'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
title: Mechanochemical pattern formation across biological scales
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: '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
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isi:
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pmid:
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call_identifier: H2020
grant_number: '771402'
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publication_identifier:
eissn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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title: Dynamic pathogen detection and social feedback shape collective hygiene in
ants
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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abstract:
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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:
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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:
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keyword:
- collective behavior
- host-pathogen interactions
- social immunity
- epidemiology
- social insects
- probabilistic modeling
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
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title: 'Data from: "Dynamic pathogen detection and social feedback shape collective
hygiene in ants" '
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)
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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
day: '28'
ddc:
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degree_awarded: PhD
department:
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- _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:
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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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- id: '9118'
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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
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file_date_updated: 2023-08-14T11:38:28Z
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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'
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creator: vkaluza
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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: '12113'
abstract:
- lang: eng
text: The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate)
(PEDOT:PSS) film can be significantly improved by optimizing the oxidation level
of the film in oxidation and reduction processes. However, precise control over
the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly
sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture
of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence
to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity
EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid
conformational change in the PEDOT:PSS films. In particular, basic amino acid
Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation
during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment
further induces highly orientated lamellar stacking microstructures to increase
σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel
trigonal-shape thermoelectric device is designed and assembled by the as-prepared
PEDOT:PSS films in order to harvest heat via a vertical temperature gradient.
An output power density of 33 μW cm−2 is generated at a temperature difference
of 40 K, showing the potential application for low-grade wearable electronic devices.
acknowledgement: Scientific Research Program Funded by Shaanxi Provincial Education
Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi
(Grant No.2022JZ-31), Young Talent fund of University Association for Science and
Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation
(Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology
(Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry
and Technology for Chemical Industry, Ministry of Education, Shaanxi University
of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi
Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology,
Shaanxi University of Science and Technology (Grant No. KFKT2022-15).
article_number: '156101'
article_processing_charge: No
article_type: original
author:
- first_name: Li
full_name: Zhang, Li
last_name: Zhang
- first_name: Xingyu
full_name: Liu, Xingyu
last_name: Liu
- first_name: Ting
full_name: Wu, Ting
last_name: Wu
- first_name: Shengduo
full_name: Xu, Shengduo
id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f
last_name: Xu
- first_name: Guoquan
full_name: Suo, Guoquan
last_name: Suo
- first_name: Xiaohui
full_name: Ye, Xiaohui
last_name: Ye
- first_name: Xiaojiang
full_name: Hou, Xiaojiang
last_name: Hou
- first_name: Yanling
full_name: Yang, Yanling
last_name: Yang
- first_name: Qingfeng
full_name: Liu, Qingfeng
last_name: Liu
- first_name: Hongqiang
full_name: Wang, Hongqiang
last_name: Wang
citation:
ama: Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance
thermoelectric device with vertical temperature gradient. Applied Surface Science.
2023;613. doi:10.1016/j.apsusc.2022.156101
apa: Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step
post-treatment to deliver high performance thermoelectric device with vertical
temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101
chicago: Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang
Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment
to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.”
Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101.
ieee: L. Zhang et al., “Two-step post-treatment to deliver high performance
thermoelectric device with vertical temperature gradient,” Applied Surface
Science, vol. 613. Elsevier, 2023.
ista: Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023.
Two-step post-treatment to deliver high performance thermoelectric device with
vertical temperature gradient. Applied Surface Science. 613, 156101.
mla: Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric
Device with Vertical Temperature Gradient.” Applied Surface Science, vol.
613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.
short: L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H.
Wang, Applied Surface Science 613 (2023).
date_created: 2023-01-12T11:55:02Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-14T11:47:06Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.apsusc.2022.156101
external_id:
isi:
- '000911497000001'
intvolume: ' 613'
isi: 1
keyword:
- Surfaces
- Coatings and Films
- Condensed Matter Physics
- Surfaces and Interfaces
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '03'
oa_version: None
publication: Applied Surface Science
publication_identifier:
issn:
- 0169-4332
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-step post-treatment to deliver high performance thermoelectric device with
vertical temperature gradient
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 613
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:
- access_level: open_access
checksum: b9247827dae5544d1d19c37abe547abc
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T12:47:32Z
date_updated: 2023-08-14T12:47:32Z
file_id: '14054'
file_name: 2023_ProbabilityTheory_Cipolloni.pdf
file_size: 782278
relation: main_file
success: 1
file_date_updated: 2023-08-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 185'
isi: 1
language:
- iso: eng
month: '04'
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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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: '12172'
abstract:
- lang: eng
text: In industrial reactors and equipment, non-ideality is quite a common phenomenon
rather than an exception. These deviations from ideality impact the process's
overall efficiency and the effectiveness of the equipment. To recognize the associated
non-ideality, one needs to have enough understanding of the formulation of the
equations and in-depth knowledge of the residence time distribution (RTD) data
of real reactors. In the current work, step input and pulse input were used to
create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the
aforementioned configuration, experiments were run at various flow rates to validate
the developed characteristic equations. To produce RTD data, distilled water was
utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior
of tracer concentration exits age distribution, and cumulative fraction for each
setup and each input was plotted and experimental results were compared with perfect
behavior. Deviation of concentration exit age distribution and cumulative fractional
distribution from ideal behavior is more in pulse input as compared to a step
input. For ideal cases, the exit age distribution curve and cumulative fraction
curves are independent of the type of input. But a significant difference was
observed for the two cases, which may be due to non-measurable fluctuations in
volumetric flow rate, non-achievement of instant injection of tracer in case of
pulse input, and slight variations in the sampling period. Further, with increasing
flow rate, concentration, exit age, and cumulative fractional curves shifted upward,
and this behavior matches with the actual case.
article_processing_charge: No
article_type: original
author:
- first_name: Bushra
full_name: Khatoon, Bushra
last_name: Khatoon
- first_name: Shoaib
full_name: Kamil, Shoaib
id: 185a19af-dc7d-11ea-9b2f-8eb2201959e9
last_name: Kamil
- first_name: Hitesh
full_name: Babu, Hitesh
last_name: Babu
- first_name: M.
full_name: Siraj Alam, M.
last_name: Siraj Alam
citation:
ama: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade
CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part
1):40-47. doi:10.1016/j.matpr.2022.11.037'
apa: 'Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental
analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings.
Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037'
chicago: 'Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental
Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings.
Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.'
ieee: 'B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis
of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings,
vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.'
ista: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of
Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part
1), 40–47.'
mla: 'Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step
and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier,
2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.'
short: 'B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings
78 (2023) 40–47.'
date_created: 2023-01-12T12:11:26Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T09:08:11Z
day: '20'
department:
- _id: BjHo
doi: 10.1016/j.matpr.2022.11.037
intvolume: ' 78'
issue: Part 1
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 40-47
publication: 'Materials Today: Proceedings'
publication_identifier:
issn:
- 2214-7853
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental analysis of Cascade CSTRs with step and pulse inputs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
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'
...