---
_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: '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: '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:
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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
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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:
- access_level: open_access
checksum: 6b3354968403cb9d48cc5a83611fb571
content_type: application/pdf
creator: epeste
date_created: 2023-05-24T16:11:16Z
date_updated: 2023-05-24T16:11:16Z
file_id: '13087'
file_name: PhD_Thesis_Alexandra_Peste_final.pdf
file_size: 2152072
relation: main_file
success: 1
- access_level: closed
checksum: 8d0df94bbcf4db72c991f22503b3fd60
content_type: application/zip
creator: epeste
date_created: 2023-05-24T16:12:59Z
date_updated: 2023-05-24T16:12:59Z
file_id: '13088'
file_name: PhD_Thesis_APeste.zip
file_size: 1658293
relation: source_file
file_date_updated: 2023-05-24T16:12:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '147'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11458'
relation: part_of_dissertation
status: public
- id: '13053'
relation: part_of_dissertation
status: public
- id: '12299'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: Efficiency and generalization of sparse neural networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '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:
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checksum: d51240675fc6dc0e3f5dc0c902695d3a
content_type: application/pdf
creator: dboocock
date_created: 2023-05-17T13:39:54Z
date_updated: 2023-05-19T07:04:25Z
embargo: 2024-05-17
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
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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
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full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
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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:
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intvolume: ' 108'
issue: '4'
language:
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url: https://doi.org/10.48550/arXiv.2203.12666
month: '07'
oa: 1
oa_version: Preprint
project:
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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
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call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
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issn:
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publication_status: published
publisher: American Physical Society
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scopus_import: '1'
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title: 'Diagrammatic Monte Carlo for electronic correlation in molecules: High-order
many-body perturbation theory with low scaling'
type: journal_article
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volume: 108
year: '2023'
...
---
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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:
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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:
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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:
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- _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
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name: Epidemics in ant societies on a chip
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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---
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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
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full_name: Cremer, Sylvia
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orcid: 0000-0002-2193-3868
citation:
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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:
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first_name: Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
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first_name: Anna V
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last_name: Grasse
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first_name: Katarina
last_name: Bodova
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last_name: Tkačik
orcid: 0000-0002-6699-1455
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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
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legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
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---
_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:
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full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
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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.'
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department:
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oa: 1
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project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
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issn:
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publisher: Institute of Science and Technology Austria
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supervisor:
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full_name: Ibáñez, Maria
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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:
- access_level: open_access
checksum: 8c7b185eba5ccd92ef55c120f654222c
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:38:28Z
date_updated: 2023-08-14T11:38:28Z
file_id: '14051'
file_name: 2023_AnnalesHenriPoincare_Wirth.pdf
file_size: 554871
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:38:28Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 717-750
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature-dimension conditions for symmetric quantum Markov semigroups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '9652'
abstract:
- lang: eng
text: In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated
nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice.
We study weaker notions of equivalence of separated nets and demonstrate that
such notions also give rise to distinct equivalence classes. Put differently,
we find occurrences of particularly strong divergence of separated nets from the
integer lattice. Our approach generalises that of Burago and Kleiner and McMullen
which takes place largely in a continuous setting. Existence of irregular separated
nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞).
In the present work we obtain stronger types of non-realisable densities.
acknowledgement: 'This work was done while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics.
2023;253:501-554. doi:10.1007/s11856-022-2448-6
apa: Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel
Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6
chicago: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.”
Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.
ieee: M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal
of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.
ista: Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal
of Mathematics. 253, 501–554.
mla: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel
Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.
short: M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.
date_created: 2021-07-14T07:01:28Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:26:34Z
day: '01'
ddc:
- '515'
- '516'
department:
- _id: UlWa
doi: 10.1007/s11856-022-2448-6
external_id:
arxiv:
- '1903.05923'
isi:
- '000904950300003'
file:
- access_level: open_access
checksum: 6fa0a3207dd1d6467c309fd1bcc867d1
content_type: application/pdf
creator: vkaluza
date_created: 2021-07-14T07:41:50Z
date_updated: 2021-07-14T07:41:50Z
file_id: '9653'
file_name: separated_nets.pdf
file_size: 900422
relation: main_file
file_date_updated: 2021-07-14T07:41:50Z
has_accepted_license: '1'
intvolume: ' 253'
isi: 1
keyword:
- Lipschitz
- bilipschitz
- bounded displacement
- modulus of continuity
- separated net
- non-realisable density
- Burago--Kleiner construction
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 501-554
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly irregular separated nets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 253
year: '2023'
...
---
_id: '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: '12183'
abstract:
- lang: eng
text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with
Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii
regime, with an optimal bound on the condensate depletion. Moreover, our lower
bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann
bracketing) a lower bound for the ground state energy of N bosons in a large box
[−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions.
Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3
apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann
boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3
chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.
ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary
conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560,
2023.
ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary
conditions. Annales Henri Poincare. 24, 1505–1560.
mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.
short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.
date_created: 2023-01-15T23:00:52Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-16T11:34:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-022-01252-3
ec_funded: 1
external_id:
arxiv:
- '2205.15284'
isi:
- '000910751800002'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.15284
month: '05'
oa: 1
oa_version: Preprint
page: 1505-1560
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bose Gas in a box with Neumann boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12544'
abstract:
- lang: eng
text: Geometry is crucial in our efforts to comprehend the structures and dynamics
of biomolecules. For example, volume, surface area, and integrated mean and Gaussian
curvature of the union of balls representing a molecule are used to quantify its
interactions with the water surrounding it in the morphometric implicit solvent
models. The Alpha Shape theory provides an accurate and reliable method for computing
these geometric measures. In this paper, we derive homogeneous formulas for the
expressions of these measures and their derivatives with respect to the atomic
coordinates, and we provide algorithms that implement them into a new software
package, AlphaMol. The only variables in these formulas are the interatomic distances,
making them insensitive to translations and rotations. AlphaMol includes a sequential
algorithm and a parallel algorithm. In the parallel version, we partition the
atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree
algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented
by a buffer zone to account for atoms whose ball representations may partially
cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up
compared to an independent serial implementation when using 32 processors. For
instance, it takes 31 s to compute the geometric measures and derivatives of each
atom in a viral capsid with more than 26 million atoms on 32 Intel processors
running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant
computations, which ultimately limit the impact of using multiple processors.
AlphaMol is available as an OpenSource software.
acknowledgement: "P.K. acknowledges support from the University of California Multicampus
Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant
No.1760485). H.E. acknowledges support from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program, Grant No.
788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31,
and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access
is funded by the Austrian Science Fund (FWF)."
article_processing_charge: No
article_type: original
author:
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean,
and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346
apa: Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume,
surface area, mean, and Gaussian curvatures of molecules and their derivatives.
Journal of Chemical Information and Modeling. American Chemical Society.
https://doi.org/10.1021/acs.jcim.2c01346
chicago: Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the
Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.”
Journal of Chemical Information and Modeling. American Chemical Society,
2023. https://doi.org/10.1021/acs.jcim.2c01346.
ieee: P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface
area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal
of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society,
pp. 973–985, 2023.
ista: Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area,
mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 63(3), 973–985.
mla: Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian
Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information
and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85,
doi:10.1021/acs.jcim.2c01346.
short: P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and
Modeling 63 (2023) 973–985.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-02-13T00:00:00Z
date_updated: 2023-08-16T12:22:07Z
day: '13'
ddc:
- '510'
- '540'
department:
- _id: HeEd
doi: 10.1021/acs.jcim.2c01346
ec_funded: 1
external_id:
isi:
- '000920370700001'
pmid:
- '36638318'
file:
- access_level: open_access
checksum: 7d20562269edff1e31b9d6019d4983b0
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:21:13Z
date_updated: 2023-08-16T12:21:13Z
file_id: '14070'
file_name: 2023_JCIM_Koehl.pdf
file_size: 8069223
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:21:13Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 973-985
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Journal of Chemical Information and Modeling
publication_identifier:
eissn:
- 1549-960X
issn:
- 1549-9596
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the volume, surface area, mean, and Gaussian curvatures of molecules
and their derivatives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2023'
...
---
_id: '12543'
abstract:
- lang: eng
text: Treating sick group members is a hallmark of collective disease defence in
vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness
and epidemiology, it is still largely unknown how pathogens react to the selection
pressure imposed by care intervention. Using social insects and pathogenic fungi,
we here performed a serial passage experiment in the presence or absence of colony
members, which provide social immunity by grooming off infectious spores from
exposed individuals. We found specific effects on pathogen diversity, virulence
and transmission. Under selection of social immunity, pathogens invested into
higher spore production, but spores were less virulent. Notably, they also elicited
a lower grooming response in colony members, compared with spores from the individual
host selection lines. Chemical spore analysis suggested that the spores from social
selection lines escaped the caregivers’ detection by containing lower levels of
ergosterol, a key fungal membrane component. Experimental application of chemically
pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated
cue triggering host social immunity against fungal pathogens. By reducing this
detection cue, pathogens were able to evade the otherwise very effective collective
disease defences of their social hosts.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the
fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team
at ISTA for ant collection and experimental help, in particular H. Leitner, and
the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg
and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the
Social Immunity team for comments on the manuscript. The study was funded by the
German Research Foundation (CR118/3-1) within the Framework of the Priority Program
SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon
2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Michaela
full_name: Hönigsberger, Michaela
id: 953894f3-25bd-11ec-8556-f70a9d38ef60
last_name: Hönigsberger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Niklas
full_name: Kampleitner, Niklas
id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87
last_name: Kampleitner
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6
apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F.,
Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature
Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6
chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse,
Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt,
and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and
Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.
ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology
and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.
ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner
N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 7, 450–460.
mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology
and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.
short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N.
Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution
7 (2023) 450–460.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T11:55:48Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
- _id: LifeSc
- _id: JiFr
doi: 10.1038/s41559-023-01981-6
ec_funded: 1
external_id:
isi:
- '000924572800001'
pmid:
- '36732670'
file:
- access_level: open_access
checksum: 8244f4650a0e7aeea488d1bcd4a31702
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:54:59Z
date_updated: 2023-08-16T11:54:59Z
file_id: '14069'
file_name: 2023_NatureEcoEvo_Stock.pdf
file_size: 1600499
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:54:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 450-460
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Nature Ecology and Evolution
publication_identifier:
eissn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/
scopus_import: '1'
status: public
title: Pathogen evasion of social immunity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-16T11:44:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
- '001021692200001'
pmid:
- '37065438'
file:
- access_level: open_access
checksum: a240a041cb9b9b7c8ba93a4706674a3f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:43:33Z
date_updated: 2023-08-16T11:43:33Z
file_id: '14068'
file_name: 2023_EvLetters_Mrnjavac.pdf
file_size: 2592189
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:43:33Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12679'
abstract:
- lang: eng
text: How to generate a brain of correct size and with appropriate cell-type diversity
during development is a major question in Neuroscience. In the developing neocortex,
radial glial progenitor (RGP) cells are the main neural stem cells that produce
cortical excitatory projection neurons, glial cells, and establish the prospective
postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated
developmental program that when disrupted can result in severe cortical malformations
such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms
instructing faithful RGP lineage progression are however not well understood.
This review will summarize recent conceptual advances that contribute to our understanding
of the general principles of RGP lineage progression.
acknowledgement: "I wish to thank all current and past members of the Hippenmeyer
laboratory at ISTA for exciting discussions on the subject of this review. I apologize
to colleagues whose work I could not cite and/or discuss in the frame of the available
space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported
by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council
(ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(grant agree-ment no. 725780 LinPro) to SH."
article_number: '102695'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Hippenmeyer S. Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4).
doi:10.1016/j.conb.2023.102695'
apa: 'Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology.
Elsevier. https://doi.org/10.1016/j.conb.2023.102695'
chicago: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression:
Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology.
Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.'
ieee: 'S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex,” Current Opinion in Neurobiology, vol.
79, no. 4. Elsevier, 2023.'
ista: 'Hippenmeyer S. 2023. Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4),
102695.'
mla: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights
from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol.
79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.'
short: S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).
date_created: 2023-02-26T12:24:21Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T12:30:25Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.conb.2023.102695
ec_funded: 1
external_id:
isi:
- '000953497700001'
pmid:
- '36842274'
file:
- access_level: open_access
checksum: 4d11c4ca87e6cbc4d2ac46d3225ea615
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:29:06Z
date_updated: 2023-08-16T12:29:06Z
file_id: '14071'
file_name: 2023_CurrentOpinionNeurobio_Hippenmeyer.pdf
file_size: 1787894
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:29:06Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '4'
keyword:
- General Neuroscience
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Principles of neural stem cell lineage progression: Insights from developing
cerebral cortex'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2023'
...
---
_id: '12429'
abstract:
- lang: eng
text: In this paper, we consider traces at initial times for functions with mixed
time-space smoothness. Such results are often needed in the theory of evolution
equations. Our result extends and unifies many previous results. Our main improvement
is that we can allow general interpolation couples. The abstract results are applied
to regularity problems for fractional evolution equations and stochastic evolution
equations, where uniform trace estimates on the half-line are shown.
acknowledgement: The first author has been partially supported by the Nachwuchsring—Network
for the promotion of young scientists—at TU Kaiserslautern. The second and third
authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation
for Scientific Research (NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Nick
full_name: Lindemulder, Nick
last_name: Lindemulder
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350.
doi:10.1002/mana.202100192
apa: Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding
and its applications to evolution equations. Mathematische Nachrichten.
Wiley. https://doi.org/10.1002/mana.202100192
chicago: Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding
and Its Applications to Evolution Equations.” Mathematische Nachrichten.
Wiley, 2023. https://doi.org/10.1002/mana.202100192.
ieee: A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its
applications to evolution equations,” Mathematische Nachrichten, vol. 296,
no. 4. Wiley, pp. 1319–1350, 2023.
ista: Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.
mla: Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution
Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp.
1319–50, doi:10.1002/mana.202100192.
short: A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023)
1319–1350.
date_created: 2023-01-29T23:00:59Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T11:41:42Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1002/mana.202100192
external_id:
arxiv:
- '2104.05063'
isi:
- '000914134900001'
file:
- access_level: open_access
checksum: 6f099f1d064173784d1a27716a2cc795
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:40:02Z
date_updated: 2023-08-16T11:40:02Z
file_id: '14067'
file_name: 2023_MathNachrichten_Agresti.pdf
file_size: 449280
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:40:02Z
has_accepted_license: '1'
intvolume: ' 296'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1319-1350
publication: Mathematische Nachrichten
publication_identifier:
eissn:
- 1522-2616
issn:
- 0025-584X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the trace embedding and its applications to evolution equations
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 296
year: '2023'
...
---
_id: '12430'
abstract:
- lang: eng
text: We study the time evolution of the Nelson model in a mean-field limit in which
N nonrelativistic bosons weakly couple (with respect to the particle number) to
a positive or zero mass quantized scalar field. Our main result is the derivation
of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove
the convergence of the approximate wave function to the many-body wave function
in norm, with a convergence rate proportional to the number of corrections taken
into account in the approximation. We prove an analogous result for the unitary
propagator. As an application, we derive a simple system of partial differential
equations describing the time evolution of the first- and second-order approximations
to the one-particle reduced density matrices of the particles and the quantum
field, respectively.
article_number: '2350006'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Falconi, Marco
last_name: Falconi
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order
corrections for the regularized Nelson model. Reviews in Mathematical Physics.
2023;35(4). doi:10.1142/S0129055X2350006X
apa: Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023).
Bogoliubov dynamics and higher-order corrections for the regularized Nelson model.
Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X
chicago: Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören
P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized
Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing,
2023. https://doi.org/10.1142/S0129055X2350006X.
ieee: M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov
dynamics and higher-order corrections for the regularized Nelson model,” Reviews
in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.
ista: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics
and higher-order corrections for the regularized Nelson model. Reviews in Mathematical
Physics. 35(4), 2350006.
mla: Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for
the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35,
no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.
short: M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical
Physics 35 (2023).
date_created: 2023-01-29T23:00:59Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-16T11:47:27Z
day: '09'
department:
- _id: RoSe
doi: 10.1142/S0129055X2350006X
external_id:
arxiv:
- '2110.00458'
isi:
- '000909760300001'
intvolume: ' 35'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2110.00458'
month: '01'
oa: 1
oa_version: Preprint
publication: Reviews in Mathematical Physics
publication_identifier:
issn:
- 0129-055X
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bogoliubov dynamics and higher-order corrections for the regularized Nelson
model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T12:41:53Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-21T06:25:48Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
file:
- access_level: closed
checksum: 59b0303dc483f40a96a610a90aab7ee9
content_type: application/pdf
creator: aschauer
date_created: 2023-05-05T13:01:14Z
date_updated: 2023-05-05T13:01:14Z
embargo: 2024-05-05
embargo_to: open_access
file_id: '12907'
file_name: Thesis_Schauer_final.pdf
file_size: 31434230
relation: main_file
- access_level: closed
checksum: 25f54e12479b6adaabd129a20568e6c1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2023-05-05T13:04:15Z
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2023-05-05T13:04:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8966'
relation: part_of_dissertation
status: public
- id: '7888'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14085'
abstract:
- lang: eng
text: We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow
under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed,
unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm
in general sparse graphs with arbitrarily good approximation guarantee.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic
Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for
a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz
Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There,
he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich
Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster
and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their
insightful comments."
alternative_title:
- LIPIcs
article_number: '69'
article_processing_charge: Yes
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Goranci G, Henzinger MH. Efficient data structures for incremental exact and
approximate maximum flow. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.ICALP.2023.69'
apa: 'Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for
incremental exact and approximate maximum flow. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69'
chicago: Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for
Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.
ieee: G. Goranci and M. H. Henzinger, “Efficient data structures for incremental
exact and approximate maximum flow,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Goranci G, Henzinger MH. 2023. Efficient data structures for incremental
exact and approximate maximum flow. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 69.'
mla: Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata,
Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.
short: G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:00:49Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.69
ec_funded: 1
external_id:
unknown:
- '2211.09606'
file:
- access_level: open_access
checksum: 074177e815a1656de5d4071c7a3dffa6
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:59:05Z
date_updated: 2023-08-21T06:59:05Z
file_id: '14089'
file_name: 2023_LIPIcsICALP_Goranci.pdf
file_size: 875910
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:59:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient data structures for incremental exact and approximate maximum flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14084'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We will consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor
Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log
Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts
c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²)
samples for integer-valued distributions (ignoring some second-order terms and
parameters), We show this is optimal up to logarithmic factors. We illustrate
with improved algorithms for counting connected subgraphs and perfect matchings
in a graph."
acknowledgement: We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the
Wang-Landau algorithm and its use in physics.
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In:
50th International Colloquium on Automata, Languages, and Programming.
Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72'
apa: 'Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs
distributions. In 50th International Colloquium on Automata, Languages, and
Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72'
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” In 50th International Colloquium on Automata, Languages, and
Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
in 50th International Colloquium on Automata, Languages, and Programming,
Paderborn, Germany, 2023, vol. 261.
ista: 'Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions.
50th International Colloquium on Automata, Languages, and Programming. ICALP:
International Colloquium on Automata, Languages, and Programming, LIPIcs, vol.
261, 72.'
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.
short: D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T06:49:11Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: VlKo
doi: 10.4230/LIPIcs.ICALP.2023.72
external_id:
arxiv:
- '2007.10824'
file:
- access_level: open_access
checksum: 6dee0684245bb1c524b9c955db1e933d
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:45:16Z
date_updated: 2023-08-21T06:45:16Z
file_id: '14088'
file_name: 2023_LIPIcsICALP_Harris.pdf
file_size: 917791
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:45:16Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14086'
abstract:
- lang: eng
text: "The maximization of submodular functions have found widespread application
in areas such as machine learning, combinatorial optimization, and economics,
where practitioners often wish to enforce various constraints; the matroid constraint
has been investigated extensively due to its algorithmic properties and expressive
power. Though tight approximation algorithms for general matroid constraints exist
in theory, the running times of such algorithms typically scale quadratically,
and are not practical for truly large scale settings. Recent progress has focused
on fast algorithms for important classes of matroids given in explicit form. Currently,
nearly-linear time algorithms only exist for graphic and partition matroids [Alina
Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone
submodular maximization constrained by graphic, transversal matroids, or laminar
matroids in time near-linear in the size of their representation. Our algorithms
achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate
the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the
running time of our algorithm cannot be improved within the fast continuous greedy
framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák,
2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures
that maintain bases with approximate maximum cardinality and weight under certain
element updates. These data structures need to support a weight decrease operation
and a novel Freeze operation that allows the algorithm to freeze elements (i.e.
force to be contained) in its basis regardless of future data structure operations.
For the laminar matroid, we present a new dynamic data structure using the top
tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et
al., 2005] that maintains the maximum weight basis under insertions and deletions
of elements in O(log n) time. This data structure needs to support certain subtree
query and path update operations that are performed every insertion and deletion
that are non-trivial to handle in conjunction. For the transversal matroid the
Freeze operation corresponds to requiring the data structure to keep a certain
set S of vertices matched, a property that we call S-stability. While there is
a large body of work on dynamic matching algorithms, none are S-stable and maintain
an approximate maximum weight matching under vertex updates. We give the first
such algorithm for bipartite graphs with total running time linear (up to log
factors) in the number of edges."
acknowledgement: " Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast
Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by
NSF Award 2127781."
alternative_title:
- LIPIcs
article_number: '74'
article_processing_charge: Yes
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Paul
full_name: Liu, Paul
last_name: Liu
- first_name: Jan
full_name: Vondrák, Jan
last_name: Vondrák
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
citation:
ama: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for
several classes of matroids. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74'
apa: 'Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster
submodular maximization for several classes of matroids. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74'
chicago: Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular
Maximization for Several Classes of Matroids.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.
ieee: M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization
for several classes of matroids,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization
for several classes of matroids. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: International Colloquium on Automata, Languages, and Programming,
LIPIcs, vol. 261, 74.'
mla: Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes
of Matroids.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.
short: M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:05:47Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.74
ec_funded: 1
external_id:
arxiv:
- '2305.00122'
file:
- access_level: open_access
checksum: a5eef225014e003efbfbe4830fdd23cb
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:04:36Z
date_updated: 2023-08-21T07:04:36Z
file_id: '14090'
file_name: 2023_LIPIcsICALP_HenzingerM.pdf
file_size: 930943
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:04:36Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster submodular maximization for several classes of matroids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14083'
abstract:
- lang: eng
text: "In this work we consider the list-decodability and list-recoverability of
arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable
if every radius pn Hamming ball contains less than L codewords; (p,\U0001D4C1,L)_q-list-recoverability
is a generalization where we place radius pn Hamming balls on every point of a
combinatorial rectangle with side length \U0001D4C1 and again stipulate that there
be less than L codewords.\r\nOur main contribution is to precisely calculate the
maximum value of p for which there exist infinite families of positive rate (p,\U0001D4C1,L)_q-list-recoverable
codes, the quantity we call the zero-rate threshold. Denoting this value by p_*,
we in fact show that codes correcting a p_*+ε fraction of errors must have size
O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin
bound.\" To complement this, a standard random code with expurgation construction
shows that there exist positive rate codes correcting a p_*-ε fraction of errors.
We also follow a classical proof template (typically attributed to Elias and Bassalygo)
to derive from the zero-rate threshold other tradeoffs between rate and decoding
radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin
bound boils down to demonstrating the Schur convexity of a certain function defined
on the q-simplex as well as the convexity of a univariate function derived from
it. We remark that an earlier argument claimed similar results for q-ary list-decoding;
however, we point out that this earlier proof is flawed."
acknowledgement: "Nicolas Resch: Research supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research
and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the
National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements
YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions."
alternative_title:
- LIPIcs
article_number: '99'
article_processing_charge: Yes
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99'
apa: 'Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new
capacity bounds for list-decoding and list-recovery. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99'
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” In 50th International
Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 99.'
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” 50th International Colloquium on Automata, Languages, and
Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ICALP.2023.99.
short: N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:13Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:26:01Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.4230/LIPIcs.ICALP.2023.99
external_id:
arxiv:
- '2210.07754'
file:
- access_level: open_access
checksum: a449143fec3fbebb092cb8ef3b53c226
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:23:18Z
date_updated: 2023-08-21T07:23:18Z
file_id: '14091'
file_name: 2023_LIPIcsICALP_Resch.pdf
file_size: 1141497
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:23:18Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '12697'
abstract:
- lang: eng
text: Models for same-material contact electrification in granular media often rely
on a local charge-driving parameter whose spatial variations lead to a stochastic
origin for charge exchange. Measuring the charge transfer from individual granular
spheres after contacts with substrates of the same material, we find instead a
“global” charging behavior, coherent over the sample’s whole surface. Cleaning
and baking samples fully resets charging magnitude and direction, which indicates
the underlying global parameter is not intrinsic to the material, but acquired
from its history. Charging behavior is randomly and irreversibly affected by changes
in relative humidity, hinting at a mechanism where adsorbates, in particular,
water, are fundamental to the charge-transfer process.
acknowledgement: "We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti
for helpful discussions. This project has received funding from the European Research
Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant
Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation
program."
article_number: '098202'
article_processing_charge: No
article_type: original
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism
driven by sample history for contact electrification in granular media. Physical
Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202
apa: Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics
reveal a global mechanism driven by sample history for contact electrification
in granular media. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.130.098202
chicago: Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters. American Physical Society,
2023. https://doi.org/10.1103/physrevlett.130.098202.
ieee: G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal
a global mechanism driven by sample history for contact electrification in granular
media,” Physical Review Letters, vol. 130, no. 9. American Physical Society,
2023.
ista: Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global
mechanism driven by sample history for contact electrification in granular media.
Physical Review Letters. 130(9), 098202.
mla: Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American
Physical Society, 2023, doi:10.1103/physrevlett.130.098202.
short: G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).
date_created: 2023-02-28T12:14:46Z
date_published: 2023-03-03T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '03'
ddc:
- '530'
- '537'
department:
- _id: ScWa
doi: 10.1103/physrevlett.130.098202
ec_funded: 1
external_id:
arxiv:
- '2211.02488'
isi:
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keyword:
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- Triboelectricity
- Soft Matter
- Acoustic Levitation
- Granular Materials
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text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13175
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:13175.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-06-30T08:07:43Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-24T11:16:35Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:13175
ec_funded: 1
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keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
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project:
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call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
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call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
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full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
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abstract:
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text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12900
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12900.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-05-05T11:08:50Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-24T11:16:35Z
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ddc:
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- '535'
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keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
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record:
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full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
tmp:
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...
---
_id: '14242'
abstract:
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text: We study the problem of training and certifying adversarially robust quantized
neural networks (QNNs). Quantization is a technique for making neural networks
more efficient by running them using low-bit integer arithmetic and is therefore
commonly adopted in industry. Recent work has shown that floating-point neural
networks that have been verified to be robust can become vulnerable to adversarial
attacks after quantization, and certification of the quantized representation
is necessary to guarantee robustness. In this work, we present quantization-aware
interval bound propagation (QA-IBP), a novel method for training robust QNNs.
Inspired by advances in robust learning of non-quantized networks, our training
algorithm computes the gradient of an abstract representation of the actual network.
Unlike existing approaches, our method can handle the discrete semantics of QNNs.
Based on QA-IBP, we also develop a complete verification procedure for verifying
the adversarial robustness of QNNs, which is guaranteed to terminate and produce
a correct answer. Compared to existing approaches, the key advantage of our verification
procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate
experimentally that our approach significantly outperforms existing methods and
establish the new state-of-the-art for training and certifying the robustness
of QNNs.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research
was sponsored by the United\r\nStates Air Force Research Laboratory and the United
States Air Force Artificial Intelligence Accelerator and was accomplished under
Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained
in this document are those of the authors and should not be interpreted as representing
the official policies, either expressed or implied,\r\nof the United States Air
Force or the U.S. Government. The U.S. Government is authorized to reproduce and
distribute reprints for Government purposes notwithstanding any copyright\r\nnotation
herein. The research was also funded in part by the AI2050 program at Schmidt Futures
(Grant G-22-63172) and Capgemini SE."
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973.
doi:10.1609/aaai.v37i12.26747'
apa: 'Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D.
(2023). Quantization-aware interval bound propagation for training certifiably
robust quantized neural networks. In Proceedings of the 37th AAAI Conference
on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747'
chicago: Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger,
and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably
Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 37:14964–73. Association for the Advancement of
Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.
ieee: M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks,”
in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.
ista: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference
on Artificial Intelligence vol. 37, 14964–14973.'
mla: Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for
Training Certifiably Robust Quantized Neural Networks.” Proceedings of the
37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association
for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.
short: M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 14964–14973.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:17Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2023-09-05T07:06:14Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i12.26747
ec_funded: 1
external_id:
arxiv:
- '2211.16187'
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.16187
month: '06'
oa: 1
oa_version: Preprint
page: 14964-14973
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantization-aware interval bound propagation for training certifiably robust
quantized neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14243'
abstract:
- lang: eng
text: 'Two-player zero-sum "graph games" are central in logic, verification, and
multi-agent systems. The game proceeds by placing a token on a vertex of a graph,
and allowing the players to move it to produce an infinite path, which determines
the winner or payoff of the game. Traditionally, the players alternate turns in
moving the token. In "bidding games", however, the players have budgets and in
each turn, an auction (bidding) determines which player moves the token. So far,
bidding games have only been studied as full-information games. In this work we
initiate the study of partial-information bidding games: we study bidding games
in which a player''s initial budget is drawn from a known probability distribution.
We show that while for some bidding mechanisms and objectives, it is straightforward
to adapt the results from the full-information setting to the partial-information
setting, for others, the analysis is significantly more challenging, requires
new techniques, and gives rise to interesting results. Specifically, we study
games with "mean-payoff" objectives in combination with "poorman" bidding. We
construct optimal strategies for a partially-informed player who plays against
a fully-informed adversary. We show that, somewhat surprisingly, the "value" under
pure strategies does not necessarily exist in such games.'
acknowledgement: This research was supported in part by ISF grant no.1679/21, by the
ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable
budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679'
apa: Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with
partially-observable budgets. In Proceedings of the 37th AAAI Conference on
Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States.
https://doi.org/10.1609/aaai.v37i5.25679
chicago: Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with
Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on
Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.
ieee: G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable
budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.
ista: 'Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable
budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI:
Conference on Artificial Intelligence vol. 37, 5464–5471.'
mla: Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.”
Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol.
37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.
short: G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 2023, pp. 5464–5471.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:18Z
date_published: 2023-06-27T00:00:00Z
date_updated: 2023-09-05T08:37:00Z
day: '27'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i5.25679
ec_funded: 1
external_id:
arxiv:
- '2211.13626'
intvolume: ' 37'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1609/aaai.v37i5.25679
month: '06'
oa: 1
oa_version: Published Version
page: 5464-5471
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bidding graph games with partially-observable budgets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14241'
abstract:
- lang: eng
text: We present a technique to optimize the reflectivity of a surface while preserving
its overall shape. The naïve optimization of the mesh vertices using the gradients
of reflectivity simulations results in undesirable distortion. In contrast, our
robust formulation optimizes the surface normal as an independent variable that
bridges the reflectivity term with differential rendering, and the regularization
term with as-rigid-as-possible elastic energy. We further adaptively subdivide
the input mesh to improve the convergence. Consequently, our method can minimize
the retroreflectivity of a wide range of input shapes, resulting in sharply creased
shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by
changing the reward for the direction of the outgoing light directions, our method
can be applied to other reflectivity design tasks, such as the optimization of
architectural walls to concentrate light in a specific region. We have tested
the proposed method using light-transport simulations and real-world 3D-printed
objects.
acknowledgement: "The authors would like to thank Yuki Koyama and Takeo Igarashi for
early discussions, and Yuta Yaguchi for support in 3D printing. This research is
partially supported by the Israel Science Foundation grant number 1390/19.\r\n"
article_number: '20'
article_processing_charge: No
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization
as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association
for Computing Machinery; 2023. doi:10.1145/3588432.3591542'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper:
Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference
Proceedings. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3588432.3591542'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth
Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023
Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity
optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings,
Los Angeles, CA, United States, 2023.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity
optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH:
Computer Graphics and Interactive Techniques Conference, 20.'
mla: 'Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface
Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for
Computing Machinery, 2023, doi:10.1145/3588432.3591542.'
short: K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference
Proceedings, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-08-27T22:01:17Z
date_published: 2023-07-23T00:00:00Z
date_updated: 2023-09-05T07:22:03Z
day: '23'
department:
- _id: BeBi
doi: 10.1145/3588432.3591542
external_id:
arxiv:
- '2305.05944'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.05944
month: '07'
oa: 1
oa_version: Preprint
publication: SIGGRAPH 2023 Conference Proceedings
publication_identifier:
isbn:
- '9798400701597'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Stealth shaper: Reflectivity optimization as surface stylization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12562'
abstract:
- lang: eng
text: Presynaptic inputs determine the pattern of activation of postsynaptic neurons
in a neural circuit. Molecular and genetic pathways that regulate the selective
formation of subsets of presynaptic inputs are largely unknown, despite significant
understanding of the general process of synaptogenesis. In this study, we have
begun to identify such factors using the spinal monosynaptic stretch reflex circuit
as a model system. In this neuronal circuit, Ia proprioceptive afferents establish
monosynaptic connections with spinal motor neurons that project to the same muscle
(termed homonymous connections) or muscles with related or synergistic function.
However, monosynaptic connections are not formed with motor neurons innervating
muscles with antagonistic functions. The ETS transcription factor ER81 (also known
as ETV1) is expressed by all proprioceptive afferents, but only a small set of
motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional
mouse genetic techniques to eliminate Er81 expression selectively from motor neurons.
We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive
afferents conveying information from homonymous and synergistic muscles, with
no change observed in the connectivity pattern from antagonistic proprioceptive
afferents. In summary, these findings suggest a role for ER81 in defined motor
neuron pools to control the assembly of specific presynaptic inputs and thereby
influence the profile of activation of these motor neurons.
acknowledgement: The authors gratefully thank Dr. Silvia Arber, University of Basel
and Friedrich Miescher Institute for Biomedical Research, for support and in whose
lab the data were collected. For advice on statistical analysis, we thank Michael
Bottomley from the Statistical Consulting Center, College of Science and Mathematics,
Wright State University.
article_processing_charge: No
article_type: original
author:
- first_name: David R.
full_name: Ladle, David R.
last_name: Ladle
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced
monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology.
2023;129(3):501-512. doi:10.1152/jn.00172.2022
apa: Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons
leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal
of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022
chicago: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons
Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal
of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022.
ieee: D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads
to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal
of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512,
2023.
ista: Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to
reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology.
129(3), 501–512.
mla: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons
Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal
of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023,
pp. 501–12, doi:10.1152/jn.00172.2022.
short: D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.
date_created: 2023-02-15T14:46:14Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-09-05T12:13:34Z
day: '01'
department:
- _id: SiHi
doi: 10.1152/jn.00172.2022
external_id:
isi:
- '000957721600001'
pmid:
- '36695533'
intvolume: ' 129'
isi: 1
issue: '3'
keyword:
- Physiology
- General Neuroscience
language:
- iso: eng
month: '03'
oa_version: None
page: 501-512
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from
proprioceptive sensory neurons
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 129
year: '2023'
...
---
_id: '13310'
abstract:
- lang: eng
text: Machine-learned systems are in widespread use for making decisions about humans,
and it is important that they are fair, i.e., not biased against individuals based
on sensitive attributes. We present runtime verification of algorithmic fairness
for systems whose models are unknown, but are assumed to have a Markov chain structure.
We introduce a specification language that can model many common algorithmic fairness
properties, such as demographic parity, equal opportunity, and social burden.
We build monitors that observe a long sequence of events as generated by a given
system, and output, after each observation, a quantitative estimate of how fair
or biased the system was on that run until that point in time. The estimate is
proven to be correct modulo a variable error bound and a given confidence level,
where the error bound gets tighter as the observed sequence gets longer. Our monitors
are of two types, and use, respectively, frequentist and Bayesian statistical
inference techniques. While the frequentist monitors compute estimates that are
objectively correct with respect to the ground truth, the Bayesian monitors compute
estimates that are correct subject to a given prior belief about the system’s
model. Using a prototype implementation, we show how we can monitor if a bank
is fair in giving loans to applicants from different social backgrounds, and if
a college is fair in admitting students while maintaining a reasonable financial
burden on the society. Although they exhibit different theoretical complexities
in certain cases, in our experiments, both frequentist and Bayesian monitors took
less than a millisecond to update their verdicts after each observation.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG101020093.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mahyar
full_name: Karimi, Mahyar
id: f1dedef5-2f78-11ee-989a-c4c97bccf506
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness.
In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382.
doi:10.1007/978-3-031-37703-7_17'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring
algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382).
Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17'
chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.
ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic
fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965,
pp. 358–382.
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic
fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13965, 358–382.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer
Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.
short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 358–382.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-07-25T18:32:40Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-05T15:14:00Z
day: '18'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-37703-7_17
ec_funded: 1
external_id:
arxiv:
- '2305.15979'
file:
- access_level: open_access
checksum: ccaf94bf7d658ba012c016e11869b54c
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:11:20Z
date_updated: 2023-07-31T08:11:20Z
file_id: '13327'
file_name: 2023_LNCS_CAV_HenzingerT.pdf
file_size: 647760
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:11:20Z
has_accepted_license: '1'
intvolume: ' 13965'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 358–382
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377037'
eissn:
- 1611-3349
isbn:
- '9783031377020'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Monitoring algorithmic fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13965
year: '2023'
...
---
_id: '12205'
abstract:
- lang: eng
text: "Background: This study seeks to evaluate the impact of breast cancer (BRCA)
gene status on tumor dissemination pattern, surgical outcome and survival in a
multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian
cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data
from 190 patients were gathered retrospectively. All patients had surgery at pOC
and at least one further rOC surgery at four European high-volume centers. Patients
were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut)
and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor
presentation, surgical outcome and survival data were analyzed between the two
groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years
younger and had significantly more tumor involvement upon diagnosis. Patients
with BRCAmut disease showed higher debulking rates at all stages. Multivariate
analysis showed that only patient age had significant predictive value for complete
tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated
with optimal debulking. Patients with BRCAmut disease showed significantly prolonged
overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged
in the BRCAmut group at all stages as well, reaching statistical significance
during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a
more aggressive course of disease with earlier onset and more extensive tumor
dissemination at pOC. However, surgical outcome and OS were significantly better
in patients with BRCAmut disease compared with patients with BRCAwt disease. We
therefore propose to consider BRCAmut status in regard to patient selection for
cytoreductive surgery, especially in rOC."
acknowledgement: "E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a
participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin
Berlin and the Berlin Institute of Health. This work was supported by European Commission’s
Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen
Access funding enabled and organized by Projekt DEAL."
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome and patient survival in primary
and recurrent high-grade serous ovarian cancer: A multicenter retrospective study
by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium.
Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical
Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation
Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in
Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective
Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.”
Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.'
ieee: 'J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of
Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.'
mla: 'Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination
Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade
Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of
Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 35–45.
date_created: 2023-01-16T09:44:36Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:37Z
day: '01'
ddc:
- '610'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12459-3
external_id:
isi:
- '000852125500006'
file:
- access_level: open_access
checksum: 36a1200e1011f4b2155a8041d0308f34
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T13:01:20Z
date_updated: 2023-02-02T13:01:20Z
file_id: '12490'
file_name: 2023_AnnalsSurgicalOncology_Glajzer.pdf
file_size: 365865
relation: main_file
success: 1
file_date_updated: 2023-02-02T13:01:20Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 35-45
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12115'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '12115'
acknowledgement: This work was supported by European Commission’s Seventh Framework
Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact
of BRCA mutation status on tumor dissemination pattern, surgical outcome, and
patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC).
A multicenter, retrospective study of the ovarian cancer therapy—innovative models
prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47.
doi:10.1245/s10434-022-12681-z'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract:
Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome,
and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer
(HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative
Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology.
Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.'
ieee: 'J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp.
46–47, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern,
surgical outcome, and patient survival in primary and recurrent high-grade serous
ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer
therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical
Oncology. 30, 46–47.'
mla: 'Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status
on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary
and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective
Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS)
Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023,
pp. 46–47, doi:10.1245/s10434-022-12681-z.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 46–47.
date_created: 2023-01-12T11:56:22Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:36Z
day: '01'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12681-z
external_id:
isi:
- '000879151800001'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1245/s10434-022-12681-z
month: '01'
oa: 1
oa_version: Published Version
page: 46-47
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12205'
relation: other
status: public
scopus_import: '1'
status: public
title: 'ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome, and patient survival in primary and recurrent high-grade
serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian
cancer therapy—innovative models prolong survival (OCTIPS) consortium'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '14253'
abstract:
- lang: eng
text: Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM)
are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration
of intracellular signaling machinery near ER-PM junctions allows these domains
to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular
compartmentalization of protein kinase A (PKA) signaling also regulates essential
cellular functions, however, no specific association between PKA and ER-PM junctional
domains is known. Here, we show that in brain neurons type I PKA is directed to
Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific
anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and
ER-resident VAP proteins results in the concentration of type I PKA between stacked
ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome
enables reciprocal regulation between PKA and Ca2+ signaling machinery to support
Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal
ER-PM junctions support a receptor-independent form of PKA signaling driven by
membrane depolarization and intracellular Ca2+, allowing conversion of information
encoded in electrical signals into biochemical changes universally recognized
throughout the cell.
acknowledgement: We thank Kayla Templeton and Peter Turcanu for technical assistance,
Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin
Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn
Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for
assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful
discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also
thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used
in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648
(J.S.T.), and F32NS108519 (N.C.V.).
article_number: '5231'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicholas C.
full_name: Vierra, Nicholas C.
last_name: Vierra
- first_name: Luisa
full_name: Ribeiro-Silva, Luisa
last_name: Ribeiro-Silva
- first_name: Michael
full_name: Kirmiz, Michael
last_name: Kirmiz
- first_name: Deborah
full_name: Van Der List, Deborah
last_name: Van Der List
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Olivia A.
full_name: Mack, Olivia A.
last_name: Mack
- first_name: James
full_name: Carroll, James
last_name: Carroll
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Sue A.
full_name: Aicher, Sue A.
last_name: Aicher
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: James S.
full_name: Trimmer, James S.
last_name: Trimmer
citation:
ama: Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions
couple excitation to Ca2+-activated PKA signaling. Nature Communications.
2023;14. doi:10.1038/s41467-023-40930-6
apa: Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P.,
Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-40930-6
chicago: Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der
List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma
Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.
ieee: N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling,” Nature Communications, vol.
14. Springer Nature, 2023.
ista: Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA,
Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma
membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications.
14, 5231.
mla: Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation
to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231,
Springer Nature, 2023, doi:10.1038/s41467-023-40930-6.
short: N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A.
Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature
Communications 14 (2023).
date_created: 2023-09-03T22:01:14Z
date_published: 2023-08-26T00:00:00Z
date_updated: 2023-09-06T06:53:32Z
day: '26'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1038/s41467-023-40930-6
external_id:
pmid:
- '37633939'
file:
- access_level: open_access
checksum: 6ab8aab4e957f626a09a1c73db3388fb
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T06:50:07Z
date_updated: 2023-09-06T06:50:07Z
file_id: '14270'
file_name: 2023_NatureComm_Vierra.pdf
file_size: 9412549
relation: main_file
success: 1
file_date_updated: 2023-09-06T06:50:07Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA
signaling
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: '14259'
abstract:
- lang: eng
text: "We provide a learning-based technique for guessing a winning strategy in
a parity game originating from an LTL synthesis problem. A cheaply obtained guess
can be useful in several applications. Not only can the guessed strategy be applied
as best-effort in cases where the game’s huge size prohibits rigorous approaches,
but it can also increase the scalability of rigorous LTL synthesis in several
ways. Firstly, checking whether a guessed strategy is winning is easier than constructing
one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy
iteration faster than constructing one from scratch. Thirdly, the guess can be
used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn
contrast to previous works, we (i) reflect the highly structured logical information
in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata
translations, and (ii) learn to reflect it properly by learning from previously
solved games, bringing the solving process closer to human-like reasoning."
acknowledgement: This research was funded in part by the German Research Foundation
(DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Maximilian
full_name: Prokop, Maximilian
last_name: Prokop
- first_name: Sabine
full_name: Rieder, Sabine
last_name: Rieder
citation:
ama: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies
in LTL synthesis by semantic learning. In: 35th International Conference on
Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20'
apa: 'Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing
winning policies in LTL synthesis by semantic learning. In 35th International
Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris,
France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder.
“Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th
International Conference on Computer Aided Verification , 13964:390–414. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.
ieee: J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning
policies in LTL synthesis by semantic learning,” in 35th International Conference
on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.
ista: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies
in LTL synthesis by semantic learning. 35th International Conference on Computer
Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.'
mla: Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic
Learning.” 35th International Conference on Computer Aided Verification ,
vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.
short: J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International
Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-06T08:27:33Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37706-8_20
file:
- access_level: open_access
checksum: ed66278b61bb869e1baba3d9b9081271
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:25:50Z
date_updated: 2023-09-06T08:25:50Z
file_id: '14276'
file_name: 2023_LNCS_CAV_Kretinsky.pdf
file_size: 428354
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:25:50Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 390-414
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guessing winning policies in LTL synthesis by semantic learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14105'
abstract:
- lang: eng
text: "Despite their recent success, deep neural networks continue to perform poorly
when they encounter distribution shifts at test time. Many recently proposed approaches
try to counter this by aligning the model to the new distribution prior to inference.
With no labels available this requires unsupervised objectives to adapt the model
on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST):
a technique that takes as input a model trained on some source data and a novel
data distribution at test time, and learns invariant and robust representations
using a student-teacher framework. We find that models adapted using TeST significantly
improve over baseline testtime adaptation algorithms. TeST achieves competitive
performance to modern domain adaptation algorithms [4, 43], while having access
to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines
on two tasks:\r\nobject detection and image segmentation and find that models
adapted with TeST. We find that TeST sets the new stateof-the art for test-time
domain adaptation algorithms. "
article_processing_charge: No
author:
- first_name: Samarth
full_name: Sinha, Samarth
last_name: Sinha
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernt
full_name: Schiele, Bernt
last_name: Schiele
citation:
ama: 'Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under
distribution shift. In: 2023 IEEE/CVF Winter Conference on Applications of
Computer Vision. Institute of Electrical and Electronics Engineers; 2023.
doi:10.1109/wacv56688.2023.00278'
apa: 'Sinha, S., Gehler, P., Locatello, F., & Schiele, B. (2023). TeST: Test-time
Self-Training under distribution shift. In 2023 IEEE/CVF Winter Conference
on Applications of Computer Vision. Waikoloa, HI, United States: Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/wacv56688.2023.00278'
chicago: 'Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele.
“TeST: Test-Time Self-Training under Distribution Shift.” In 2023 IEEE/CVF
Winter Conference on Applications of Computer Vision. Institute of Electrical
and Electronics Engineers, 2023. https://doi.org/10.1109/wacv56688.2023.00278.'
ieee: 'S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training
under distribution shift,” in 2023 IEEE/CVF Winter Conference on Applications
of Computer Vision, Waikoloa, HI, United States, 2023.'
ista: 'Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training
under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer
Vision. WACV: Winter Conference on Applications of Computer Vision.'
mla: 'Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.”
2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute
of Electrical and Electronics Engineers, 2023, doi:10.1109/wacv56688.2023.00278.'
short: S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter
Conference on Applications of Computer Vision, Institute of Electrical and Electronics
Engineers, 2023.
conference:
end_date: 2023-01-07
location: Waikoloa, HI, United States
name: 'WACV: Winter Conference on Applications of Computer Vision'
start_date: 2023-01-02
date_created: 2023-08-21T12:11:38Z
date_published: 2023-02-06T00:00:00Z
date_updated: 2023-09-06T10:26:56Z
day: '06'
department:
- _id: FrLo
doi: 10.1109/wacv56688.2023.00278
extern: '1'
external_id:
arxiv:
- '2209.11459'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.11459
month: '02'
oa: 1
oa_version: Preprint
publication: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision
publication_identifier:
eissn:
- 2642-9381
isbn:
- '9781665493475'
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'TeST: Test-time Self-Training under distribution shift'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14256'
abstract:
- lang: eng
text: "Context. Space asteroseismology is revolutionizing our knowledge of the internal
structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries
of signatures of strong magnetic fields in the core of red giant stars. The key
signature for such a detection is the asymmetry these fields induce in the frequency
splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate
the ability of the observed asymmetries of the frequency splittings of dipolar
mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods.
We used the powerful analytical Racah-Wigner algebra used in quantum mechanics
to characterize the geometrical couplings of dipolar mixed oscillation modes with
various realistically plausible topologies of fossil magnetic fields. We also
computed the induced perturbation of their frequencies.\r\nResults. First, in
the case of an oblique magnetic dipole, we provide the exact analytical expression
of the asymmetry as a function of the angle between the rotation and magnetic
axes. Its value provides a direct measure of this angle. Second, considering a
combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry
is blind to the unraveling of the relative strength and sign of each component.
Finally, in the case of a given multipole, we show that a negative asymmetry is
a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar
mixed modes provide a key bit of information on the geometrical topology of deep
fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints
should therefore be combined with spectropolarimetric observations and numerical
simulations, which aim to predict the more probable stable large-scale geometries."
acknowledgement: The authors are grateful to the referee for her/his detailed and
constructive report, which has allowed us to improve our article. S. M. acknowledges
support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU).
We thank R. A. Garcia for fruitful discussions and suggestions.
article_number: L9
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
author:
- first_name: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: 'Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed
modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
2023;676. doi:10.1051/0004-6361/202346832'
apa: 'Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings
of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy
and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832'
chicago: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.'
ieee: 'S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields,” Astronomy and
Astrophysics, vol. 676. EDP Sciences, 2023.'
ista: 'Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
676, L9.'
mla: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.'
short: S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-09-06T11:05:58Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202346832
external_id:
arxiv:
- '2306.11587'
isi:
- '001046037700007'
file:
- access_level: open_access
checksum: 7b30d26fb2b7bcb5b5be1414950615f9
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:13:19Z
date_updated: 2023-09-06T07:13:19Z
file_id: '14271'
file_name: 2023_AstronomyAstrophysics_Mathis.pdf
file_size: 458120
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:13:19Z
has_accepted_license: '1'
intvolume: ' 676'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Asymmetries of frequency splittings of dipolar mixed modes: A window on the
topology of deep magnetic 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 676
year: '2023'
...
---
_id: '14208'
abstract:
- lang: eng
text: This paper focuses on over-parameterized deep neural networks (DNNs) with
ReLU activation functions and proves that when the data distribution is well-separated,
DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly)
zero-training error under the lazy training regime. For this purpose, we unify
three interrelated concepts of overparameterization, benign overfitting, and the
Lipschitz constant of DNNs. Our results indicate that interpolating with smoother
functions leads to better generalization. Furthermore, we investigate the special
case where interpolating smooth ground-truth functions is performed by DNNs under
the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates
that the generalization error converges to a constant order that only depends
on label noise and initialization noise, which theoretically verifies benign overfitting.
Our analysis provides a tight lower bound on the normalized margin under non-smooth
activation functions, as well as the minimum eigenvalue of NTK under high-dimensional
settings, which has its own interest in learning theory.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Zhenyu
full_name: Zhu, Zhenyu
last_name: Zhu
- first_name: Fanghui
full_name: Liu, Fanghui
last_name: Liu
- first_name: Grigorios G
full_name: Chrysos, Grigorios G
last_name: Chrysos
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. Benign overfitting in deep
neural networks under lazy training. In: Proceedings of the 40th International
Conference on Machine Learning. Vol 202. ML Research Press; 2023:43105-43128.'
apa: 'Zhu, Z., Liu, F., Chrysos, G. G., Locatello, F., & Cevher, V. (2023).
Benign overfitting in deep neural networks under lazy training. In Proceedings
of the 40th International Conference on Machine Learning (Vol. 202, pp. 43105–43128).
Honolulu, Hawaii, United States: ML Research Press.'
chicago: Zhu, Zhenyu, Fanghui Liu, Grigorios G Chrysos, Francesco Locatello, and
Volkan Cevher. “Benign Overfitting in Deep Neural Networks under Lazy Training.”
In Proceedings of the 40th International Conference on Machine Learning,
202:43105–28. ML Research Press, 2023.
ieee: Z. Zhu, F. Liu, G. G. Chrysos, F. Locatello, and V. Cevher, “Benign overfitting
in deep neural networks under lazy training,” in Proceedings of the 40th International
Conference on Machine Learning, Honolulu, Hawaii, United States, 2023, vol.
202, pp. 43105–43128.
ista: Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. 2023. Benign overfitting
in deep neural networks under lazy training. Proceedings of the 40th International
Conference on Machine Learning. International Conference on Machine Learning,
PMLR, vol. 202, 43105–43128.
mla: Zhu, Zhenyu, et al. “Benign Overfitting in Deep Neural Networks under Lazy
Training.” Proceedings of the 40th International Conference on Machine Learning,
vol. 202, ML Research Press, 2023, pp. 43105–28.
short: Z. Zhu, F. Liu, G.G. Chrysos, F. Locatello, V. Cevher, in:, Proceedings of
the 40th International Conference on Machine Learning, ML Research Press, 2023,
pp. 43105–43128.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, United States
name: International Conference on Machine Learning
start_date: 2023-07-23
date_created: 2023-08-22T14:18:18Z
date_published: 2023-05-30T00:00:00Z
date_updated: 2023-09-13T08:46:46Z
day: '30'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2305.19377'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.19377
month: '05'
oa: 1
oa_version: Preprint
page: 43105-43128
publication: Proceedings of the 40th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: Benign overfitting in deep neural networks under lazy training
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14209'
abstract:
- lang: eng
text: Diffusion models excel at generating photorealistic images from text-queries.
Naturally, many approaches have been proposed to use these generative abilities
to augment training datasets for downstream tasks, such as classification. However,
diffusion models are themselves trained on large noisily supervised, but nonetheless,
annotated datasets. It is an open question whether the generalization capabilities
of diffusion models beyond using the additional data of the pre-training process
for augmentation lead to improved downstream performance. We perform a systematic
evaluation of existing methods to generate images from diffusion models and study
new extensions to assess their benefit for data augmentation. While we find that
personalizing diffusion models towards the target data outperforms simpler prompting
strategies, we also show that using the training data of the diffusion model alone,
via a simple nearest neighbor retrieval procedure, leads to even stronger downstream
performance. Overall, our study probes the limitations of diffusion models for
data augmentation but also highlights its potential in generating new training
data to improve performance on simple downstream vision tasks.
article_number: '2304.10253'
article_processing_charge: No
author:
- first_name: Max F.
full_name: Burg, Max F.
last_name: Burg
- first_name: Florian
full_name: Wenzel, Florian
last_name: Wenzel
- first_name: Dominik
full_name: Zietlow, Dominik
last_name: Zietlow
- first_name: Max
full_name: Horn, Max
last_name: Horn
- first_name: Osama
full_name: Makansi, Osama
last_name: Makansi
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Chris
full_name: Russell, Chris
last_name: Russell
citation:
ama: Burg MF, Wenzel F, Zietlow D, et al. A data augmentation perspective on diffusion
models and retrieval. arXiv. doi:10.48550/arXiv.2304.10253
apa: Burg, M. F., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F.,
& Russell, C. (n.d.). A data augmentation perspective on diffusion models
and retrieval. arXiv. https://doi.org/10.48550/arXiv.2304.10253
chicago: Burg, Max F., Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi,
Francesco Locatello, and Chris Russell. “A Data Augmentation Perspective on Diffusion
Models and Retrieval.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.10253.
ieee: M. F. Burg et al., “A data augmentation perspective on diffusion models
and retrieval,” arXiv. .
ista: Burg MF, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. A
data augmentation perspective on diffusion models and retrieval. arXiv, 2304.10253.
mla: Burg, Max F., et al. “A Data Augmentation Perspective on Diffusion Models and
Retrieval.” ArXiv, 2304.10253, doi:10.48550/arXiv.2304.10253.
short: M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell,
ArXiv (n.d.).
date_created: 2023-08-22T14:18:43Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-09-13T08:51:56Z
day: '20'
department:
- _id: FrLo
doi: 10.48550/arXiv.2304.10253
extern: '1'
external_id:
arxiv:
- '2304.10253'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.10253
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: A data augmentation perspective on diffusion models and retrieval
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14211'
abstract:
- lang: eng
text: 'Causal discovery methods are intrinsically constrained by the set of assumptions
needed to ensure structure identifiability. Moreover additional restrictions are
often imposed in order to simplify the inference task: this is the case for the
Gaussian noise assumption on additive non-linear models, which is common to many
causal discovery approaches. In this paper we show the shortcomings of inference
under this hypothesis, analyzing the risk of edge inversion under violation of
Gaussianity of the noise terms. Then, we propose a novel method for inferring
the topological ordering of the variables in the causal graph, from data generated
according to an additive non-linear model with a generic noise distribution. This
leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm
with a minimal set of assumptions and state of the art performance, experimentally
benchmarked on synthetic data.'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Montagna, Francesco
last_name: Montagna
- first_name: Nicoletta
full_name: Noceti, Nicoletta
last_name: Noceti
- first_name: Lorenzo
full_name: Rosasco, Lorenzo
last_name: Rosasco
- first_name: Kun
full_name: Zhang, Kun
last_name: Zhang
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Causal discovery with
score matching on additive models with arbitrary noise. In: 2nd Conference
on Causal Learning and Reasoning. ; 2023.'
apa: Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023).
Causal discovery with score matching on additive models with arbitrary noise.
In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.
chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and
Francesco Locatello. “Causal Discovery with Score Matching on Additive Models
with Arbitrary Noise.” In 2nd Conference on Causal Learning and Reasoning,
2023.
ieee: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Causal discovery
with score matching on additive models with arbitrary noise,” in 2nd Conference
on Causal Learning and Reasoning, Tübingen, Germany, 2023.
ista: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Causal discovery
with score matching on additive models with arbitrary noise. 2nd Conference on
Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.'
mla: Montagna, Francesco, et al. “Causal Discovery with Score Matching on Additive
Models with Arbitrary Noise.” 2nd Conference on Causal Learning and Reasoning,
2023.
short: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference
on Causal Learning and Reasoning, 2023.
conference:
end_date: 2023-04-14
location: Tübingen, Germany
name: 'CLeaR: Conference on Causal Learning and Reasoning'
start_date: 2023-04-11
date_created: 2023-08-22T14:19:21Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-09-13T09:00:31Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2304.03265'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2304.03265
month: '04'
oa: 1
oa_version: Preprint
publication: 2nd Conference on Causal Learning and Reasoning
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Causal discovery with score matching on additive models with arbitrary noise
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14212'
abstract:
- lang: eng
text: This paper demonstrates how to discover the whole causal graph from the second
derivative of the log-likelihood in observational non-linear additive Gaussian
noise models. Leveraging scalable machine learning approaches to approximate the
score function ∇logp(X), we extend the work of Rolland et al. (2022) that only
recovers the topological order from the score and requires an expensive pruning
step removing spurious edges among those admitted by the ordering. Our analysis
leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces
the complexity of the pruning by a factor proportional to the graph size. In practice,
DAS achieves competitive accuracy with current state-of-the-art while being over
an order of magnitude faster. Overall, our approach enables principled and scalable
causal discovery, significantly lowering the compute bar.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Montagna, Francesco
last_name: Montagna
- first_name: Nicoletta
full_name: Noceti, Nicoletta
last_name: Noceti
- first_name: Lorenzo
full_name: Rosasco, Lorenzo
last_name: Rosasco
- first_name: Kun
full_name: Zhang, Kun
last_name: Zhang
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Scalable causal discovery
with score matching. In: 2nd Conference on Causal Learning and Reasoning.
; 2023.'
apa: Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023).
Scalable causal discovery with score matching. In 2nd Conference on Causal
Learning and Reasoning. Tübingen, Germany.
chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and
Francesco Locatello. “Scalable Causal Discovery with Score Matching.” In 2nd
Conference on Causal Learning and Reasoning, 2023.
ieee: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Scalable
causal discovery with score matching,” in 2nd Conference on Causal Learning
and Reasoning, Tübingen, Germany, 2023.
ista: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Scalable causal
discovery with score matching. 2nd Conference on Causal Learning and Reasoning.
CLeaR: Conference on Causal Learning and Reasoning.'
mla: Montagna, Francesco, et al. “Scalable Causal Discovery with Score Matching.”
2nd Conference on Causal Learning and Reasoning, 2023.
short: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference
on Causal Learning and Reasoning, 2023.
conference:
end_date: 2023-04-14
location: Tübingen, Germany
name: 'CLeaR: Conference on Causal Learning and Reasoning'
start_date: 2023-04-11
date_created: 2023-08-22T14:19:40Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-09-13T09:03:24Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2304.03382'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2304.03382
month: '04'
oa: 1
oa_version: Preprint
publication: 2nd Conference on Causal Learning and Reasoning
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable causal discovery with score matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14214'
abstract:
- lang: eng
text: 'Recent years have seen a surge of interest in learning high-level causal
representations from low-level image pairs under interventions. Yet, existing
efforts are largely limited to simple synthetic settings that are far away from
real-world problems. In this paper, we present Causal Triplet, a causal representation
learning benchmark featuring not only visually more complex scenes, but also two
crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual
setting, where only certain object-level variables allow for counterfactual observations
whereas others do not; (ii) an interventional downstream task with an emphasis
on out-of-distribution robustness from the independent causal mechanisms principle.
Through extensive experiments, we find that models built with the knowledge of
disentangled or object-centric representations significantly outperform their
distributed counterparts. However, recent causal representation learning methods
still struggle to identify such latent structures, indicating substantial challenges
and opportunities for future work.'
article_processing_charge: No
author:
- first_name: Yuejiang
full_name: Liu, Yuejiang
last_name: Liu
- first_name: Alexandre
full_name: Alahi, Alexandre
last_name: Alahi
- first_name: Chris
full_name: Russell, Chris
last_name: Russell
- first_name: Max
full_name: Horn, Max
last_name: Horn
- first_name: Dominik
full_name: Zietlow, Dominik
last_name: Zietlow
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Liu Y, Alahi A, Russell C, et al. Causal triplet: An open challenge for intervention-centric
causal representation learning. In: 2nd Conference on Causal Learning and Reasoning.
; 2023.'
apa: 'Liu, Y., Alahi, A., Russell, C., Horn, M., Zietlow, D., Schölkopf, B., &
Locatello, F. (2023). Causal triplet: An open challenge for intervention-centric
causal representation learning. In 2nd Conference on Causal Learning and Reasoning.
Tübingen, Germany.'
chicago: 'Liu, Yuejiang, Alexandre Alahi, Chris Russell, Max Horn, Dominik Zietlow,
Bernhard Schölkopf, and Francesco Locatello. “Causal Triplet: An Open Challenge
for Intervention-Centric Causal Representation Learning.” In 2nd Conference
on Causal Learning and Reasoning, 2023.'
ieee: 'Y. Liu et al., “Causal triplet: An open challenge for intervention-centric
causal representation learning,” in 2nd Conference on Causal Learning and Reasoning,
Tübingen, Germany, 2023.'
ista: 'Liu Y, Alahi A, Russell C, Horn M, Zietlow D, Schölkopf B, Locatello F. 2023.
Causal triplet: An open challenge for intervention-centric causal representation
learning. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on
Causal Learning and Reasoning.'
mla: 'Liu, Yuejiang, et al. “Causal Triplet: An Open Challenge for Intervention-Centric
Causal Representation Learning.” 2nd Conference on Causal Learning and Reasoning,
2023.'
short: Y. Liu, A. Alahi, C. Russell, M. Horn, D. Zietlow, B. Schölkopf, F. Locatello,
in:, 2nd Conference on Causal Learning and Reasoning, 2023.
conference:
end_date: 2023-04-14
location: Tübingen, Germany
name: 'CLeaR: Conference on Causal Learning and Reasoning'
start_date: 2023-04-11
date_created: 2023-08-22T14:20:18Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2023-09-13T09:23:08Z
day: '12'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2301.05169'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.05169
month: '04'
oa: 1
oa_version: Preprint
publication: 2nd Conference on Causal Learning and Reasoning
publication_status: published
quality_controlled: '1'
status: public
title: 'Causal triplet: An open challenge for intervention-centric causal representation
learning'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14217'
abstract:
- lang: eng
text: 'Neural networks embed the geometric structure of a data manifold lying in
a high-dimensional space into latent representations. Ideally, the distribution
of the data points in the latent space should depend only on the task, the data,
the loss, and other architecture-specific constraints. However, factors such as
the random weights initialization, training hyperparameters, or other sources
of randomness in the training phase may induce incoherent latent spaces that hinder
any form of reuse. Nevertheless, we empirically observe that, under the same data
and modeling choices, the angles between the encodings within distinct latent
spaces do not change. In this work, we propose the latent similarity between each
sample and a fixed set of anchors as an alternative data representation, demonstrating
that it can enforce the desired invariances without any additional training. We
show how neural architectures can leverage these relative representations to guarantee,
in practice, invariance to latent isometries and rescalings, effectively enabling
latent space communication: from zero-shot model stitching to latent space comparison
between diverse settings. We extensively validate the generalization capability
of our approach on different datasets, spanning various modalities (images, text,
graphs), tasks (e.g., classification, reconstruction) and architectures (e.g.,
CNNs, GCNs, transformers).'
article_processing_charge: No
author:
- first_name: Luca
full_name: Moschella, Luca
last_name: Moschella
- first_name: Valentino
full_name: Maiorca, Valentino
last_name: Maiorca
- first_name: Marco
full_name: Fumero, Marco
last_name: Fumero
- first_name: Antonio
full_name: Norelli, Antonio
last_name: Norelli
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Emanuele
full_name: Rodolà, Emanuele
last_name: Rodolà
citation:
ama: 'Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. Relative
representations enable zero-shot latent space communication. In: The 11th International
Conference on Learning Representations. ; 2023.'
apa: Moschella, L., Maiorca, V., Fumero, M., Norelli, A., Locatello, F., & Rodolà,
E. (2023). Relative representations enable zero-shot latent space communication.
In The 11th International Conference on Learning Representations. Kigali,
Rwanda.
chicago: Moschella, Luca, Valentino Maiorca, Marco Fumero, Antonio Norelli, Francesco
Locatello, and Emanuele Rodolà. “Relative Representations Enable Zero-Shot Latent
Space Communication.” In The 11th International Conference on Learning Representations,
2023.
ieee: L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, and E. Rodolà,
“Relative representations enable zero-shot latent space communication,” in The
11th International Conference on Learning Representations, Kigali, Rwanda,
2023.
ista: Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. 2023.
Relative representations enable zero-shot latent space communication. The 11th
International Conference on Learning Representations. International Conference
on Machine Learning Representations.
mla: Moschella, Luca, et al. “Relative Representations Enable Zero-Shot Latent Space
Communication.” The 11th International Conference on Learning Representations,
2023.
short: L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, E. Rodolà,
in:, The 11th International Conference on Learning Representations, 2023.
conference:
end_date: 2023-05-05
location: Kigali, Rwanda
name: International Conference on Machine Learning Representations
start_date: 2023-05-01
date_created: 2023-08-22T14:22:20Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-09-13T09:44:26Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2209.15430'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.15430
month: '05'
oa: 1
oa_version: Preprint
publication: The 11th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: Relative representations enable zero-shot latent space communication
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14222'
abstract:
- lang: eng
text: Learning generative object models from unlabelled videos is a long standing
problem and required for causal scene modeling. We decompose this problem into
three easier subtasks, and provide candidate solutions for each of them. Inspired
by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks
of moving objects via unsupervised motion segmentation. Second, generative models
are trained on the masks of the background and the moving objects, respectively.
Third, background and foreground models are combined in a conditional "dead leaves"
scene model to sample novel scene configurations where occlusions and depth layering
arise naturally. To evaluate the individual stages, we introduce the Fishbowl
dataset positioned between complex real-world scenes and common object-centric
benchmarks of simplistic objects. We show that our approach allows learning generative
models that generalize beyond the occlusions present in the input videos, and
represent scenes in a modular fashion that allows sampling plausible scenes outside
the training distribution by permitting, for instance, object numbers or densities
not observed in the training set.
article_number: '2110.06562'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Tangemann, Matthias
last_name: Tangemann
- first_name: Steffen
full_name: Schneider, Steffen
last_name: Schneider
- first_name: Julius von
full_name: Kügelgen, Julius von
last_name: Kügelgen
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Thomas
full_name: Brox, Thomas
last_name: Brox
- first_name: Matthias
full_name: Kümmerer, Matthias
last_name: Kümmerer
- first_name: Matthias
full_name: Bethge, Matthias
last_name: Bethge
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Tangemann M, Schneider S, Kügelgen J von, et al. Unsupervised object learning
via common fate. In: 2nd Conference on Causal Learning and Reasoning. ;
2023.'
apa: Tangemann, M., Schneider, S., Kügelgen, J. von, Locatello, F., Gehler, P.,
Brox, T., … Schölkopf, B. (2023). Unsupervised object learning via common fate.
In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.
chicago: Tangemann, Matthias, Steffen Schneider, Julius von Kügelgen, Francesco
Locatello, Peter Gehler, Thomas Brox, Matthias Kümmerer, Matthias Bethge, and
Bernhard Schölkopf. “Unsupervised Object Learning via Common Fate.” In 2nd
Conference on Causal Learning and Reasoning, 2023.
ieee: M. Tangemann et al., “Unsupervised object learning via common fate,”
in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany,
2023.
ista: 'Tangemann M, Schneider S, Kügelgen J von, Locatello F, Gehler P, Brox T,
Kümmerer M, Bethge M, Schölkopf B. 2023. Unsupervised object learning via common
fate. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal
Learning and Reasoning, 2110.06562.'
mla: Tangemann, Matthias, et al. “Unsupervised Object Learning via Common Fate.”
2nd Conference on Causal Learning and Reasoning, 2110.06562, 2023.
short: M. Tangemann, S. Schneider, J. von Kügelgen, F. Locatello, P. Gehler, T.
Brox, M. Kümmerer, M. Bethge, B. Schölkopf, in:, 2nd Conference on Causal Learning
and Reasoning, 2023.
conference:
end_date: 2023-04-14
location: Tübingen, Germany
name: 'CLeaR: Conference on Causal Learning and Reasoning'
start_date: 2023-04-11
date_created: 2023-08-22T14:23:54Z
date_published: 2023-04-15T00:00:00Z
date_updated: 2023-09-13T11:31:14Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2110.06562'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2110.06562
month: '04'
oa: 1
oa_version: Preprint
publication: 2nd Conference on Causal Learning and Reasoning
publication_status: published
quality_controlled: '1'
status: public
title: Unsupervised object learning via common fate
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14218'
abstract:
- lang: eng
text: Humans naturally decompose their environment into entities at the appropriate
level of abstraction to act in the world. Allowing machine learning algorithms
to derive this decomposition in an unsupervised way has become an important line
of research. However, current methods are restricted to simulated data or require
additional information in the form of motion or depth in order to successfully
discover objects. In this work, we overcome this limitation by showing that reconstructing
features from models trained in a self-supervised manner is a sufficient training
signal for object-centric representations to arise in a fully unsupervised way.
Our approach, DINOSAUR, significantly out-performs existing image-based object-centric
learning models on simulated data and is the first unsupervised object-centric
model that scales to real-world datasets such as COCO and PASCAL VOC. DINOSAUR
is conceptually simple and shows competitive performance compared to more involved
pipelines from the computer vision literature.
article_processing_charge: No
author:
- first_name: Maximilian
full_name: Seitzer, Maximilian
last_name: Seitzer
- first_name: Max
full_name: Horn, Max
last_name: Horn
- first_name: Andrii
full_name: Zadaianchuk, Andrii
last_name: Zadaianchuk
- first_name: Dominik
full_name: Zietlow, Dominik
last_name: Zietlow
- first_name: Tianjun
full_name: Xiao, Tianjun
last_name: Xiao
- first_name: Carl-Johann Simon-Gabriel
full_name: Carl-Johann Simon-Gabriel, Carl-Johann Simon-Gabriel
last_name: Carl-Johann Simon-Gabriel
- first_name: Tong
full_name: He, Tong
last_name: He
- first_name: Zheng
full_name: Zhang, Zheng
last_name: Zhang
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Thomas
full_name: Brox, Thomas
last_name: Brox
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Seitzer M, Horn M, Zadaianchuk A, et al. Bridging the gap to real-world object-centric
learning. In: The 11th International Conference on Learning Representations.
; 2023.'
apa: Seitzer, M., Horn, M., Zadaianchuk, A., Zietlow, D., Xiao, T., Carl-Johann
Simon-Gabriel, C.-J. S.-G., … Locatello, F. (2023). Bridging the gap to real-world
object-centric learning. In The 11th International Conference on Learning Representations.
Kigali, Rwanda.
chicago: Seitzer, Maximilian, Max Horn, Andrii Zadaianchuk, Dominik Zietlow, Tianjun
Xiao, Carl-Johann Simon-Gabriel Carl-Johann Simon-Gabriel, Tong He, et al. “Bridging
the Gap to Real-World Object-Centric Learning.” In The 11th International Conference
on Learning Representations, 2023.
ieee: M. Seitzer et al., “Bridging the gap to real-world object-centric learning,”
in The 11th International Conference on Learning Representations, Kigali,
Rwanda, 2023.
ista: 'Seitzer M, Horn M, Zadaianchuk A, Zietlow D, Xiao T, Carl-Johann Simon-Gabriel
C-JS-G, He T, Zhang Z, Schölkopf B, Brox T, Locatello F. 2023. Bridging the gap
to real-world object-centric learning. The 11th International Conference on Learning
Representations. ICLR: International Conference on Learning Representations.'
mla: Seitzer, Maximilian, et al. “Bridging the Gap to Real-World Object-Centric
Learning.” The 11th International Conference on Learning Representations,
2023.
short: M. Seitzer, M. Horn, A. Zadaianchuk, D. Zietlow, T. Xiao, C.-J.S.-G. Carl-Johann
Simon-Gabriel, T. He, Z. Zhang, B. Schölkopf, T. Brox, F. Locatello, in:, The
11th International Conference on Learning Representations, 2023.
conference:
end_date: 2023-05-05
location: Kigali, Rwanda
name: 'ICLR: International Conference on Learning Representations'
start_date: 2023-05-01
date_created: 2023-08-22T14:22:41Z
date_published: 2023-05-10T00:00:00Z
date_updated: 2023-09-13T11:37:03Z
day: '10'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2209.14860'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.14860
month: '05'
oa: 1
oa_version: Preprint
publication: The 11th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: Bridging the gap to real-world object-centric learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14219'
abstract:
- lang: eng
text: "In this paper, we show that recent advances in self-supervised feature\r\nlearning
enable unsupervised object discovery and semantic segmentation with a\r\nperformance
that matches the state of the field on supervised semantic\r\nsegmentation 10
years ago. We propose a methodology based on unsupervised\r\nsaliency masks and
self-supervised feature clustering to kickstart object\r\ndiscovery followed by
training a semantic segmentation network on pseudo-labels\r\nto bootstrap the
system on images with multiple objects. We present results on\r\nPASCAL VOC that
go far beyond the current state of the art (50.0 mIoU), and we\r\nreport for the
first time results on MS COCO for the whole set of 81 classes:\r\nour method discovers
34 categories with more than $20\\%$ IoU, while obtaining\r\nan average IoU of
19.6 for all 81 categories."
article_processing_charge: No
author:
- first_name: Andrii
full_name: Zadaianchuk, Andrii
last_name: Zadaianchuk
- first_name: Matthaeus
full_name: Kleindessner, Matthaeus
last_name: Kleindessner
- first_name: Yi
full_name: Zhu, Yi
last_name: Zhu
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Thomas
full_name: Brox, Thomas
last_name: Brox
citation:
ama: 'Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. Unsupervised semantic
segmentation with self-supervised object-centric representations. In: The 11th
International Conference on Learning Representations. ; 2023.'
apa: Zadaianchuk, A., Kleindessner, M., Zhu, Y., Locatello, F., & Brox, T. (2023).
Unsupervised semantic segmentation with self-supervised object-centric representations.
In The 11th International Conference on Learning Representations. Kigali,
Rwanda.
chicago: Zadaianchuk, Andrii, Matthaeus Kleindessner, Yi Zhu, Francesco Locatello,
and Thomas Brox. “Unsupervised Semantic Segmentation with Self-Supervised Object-Centric
Representations.” In The 11th International Conference on Learning Representations,
2023.
ieee: A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, and T. Brox, “Unsupervised
semantic segmentation with self-supervised object-centric representations,” in
The 11th International Conference on Learning Representations, Kigali,
Rwanda, 2023.
ista: 'Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. 2023. Unsupervised
semantic segmentation with self-supervised object-centric representations. The
11th International Conference on Learning Representations. ICLR: International
Conference on Learning Representations.'
mla: Zadaianchuk, Andrii, et al. “Unsupervised Semantic Segmentation with Self-Supervised
Object-Centric Representations.” The 11th International Conference on Learning
Representations, 2023.
short: A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, T. Brox, in:, The
11th International Conference on Learning Representations, 2023.
conference:
end_date: 2023-05-05
location: Kigali, Rwanda
name: 'ICLR: International Conference on Learning Representations'
start_date: 2023-05-01
date_created: 2023-08-22T14:22:58Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-09-13T11:25:43Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2207.05027'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2207.05027
month: '05'
oa: 1
oa_version: Preprint
publication: The 11th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: Unsupervised semantic segmentation with self-supervised object-centric representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14333'
abstract:
- lang: eng
text: "As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly
only evaluated on simulated data. This is concerning, given that\r\nsimulations
reflect common preconceptions about generating processes regarding\r\nnoise distributions,
model classes, and more. In this work, we propose a novel\r\nmethod for falsifying
the output of a causal discovery algorithm in the absence\r\nof ground truth.
Our key insight is that while statistical learning seeks\r\nstability across subsets
of data points, causal learning should seek stability\r\nacross subsets of variables.
Motivated by this insight, our method relies on a\r\nnotion of compatibility between
causal graphs learned on different subsets of\r\nvariables. We prove that detecting
incompatibilities can falsify wrongly\r\ninferred causal relations due to violation
of assumptions or errors from finite\r\nsample effects. Although passing such
compatibility tests is only a necessary\r\ncriterion for good performance, we
argue that it provides strong evidence for\r\nthe causal models whenever compatibility
entails strong implications for the\r\njoint distribution. We also demonstrate
experimentally that detection of\r\nincompatibilities can aid in causal model
selection."
article_number: '2307.09552'
article_processing_charge: No
author:
- first_name: Philipp M.
full_name: Faller, Philipp M.
last_name: Faller
- first_name: Leena Chennuru
full_name: Vankadara, Leena Chennuru
last_name: Vankadara
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
citation:
ama: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552'
apa: 'Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing,
D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth.
arXiv. https://doi.org/10.48550/arXiv.2307.09552'
chicago: 'Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri,
Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal
Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.'
ieee: 'P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing,
“Self-compatibility: Evaluating causal discovery without ground truth,” arXiv.
.'
ista: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility:
Evaluating causal discovery without ground truth. arXiv, 2307.09552.'
mla: 'Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery
without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.'
short: P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv
(n.d.).
date_created: 2023-09-13T12:44:59Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-13T12:47:53Z
day: '18'
department:
- _id: FrLo
doi: 10.48550/arXiv.2307.09552
extern: '1'
external_id:
arxiv:
- '2307.09552'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.09552
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Self-compatibility: Evaluating causal discovery without ground truth'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14277'
abstract:
- lang: eng
text: Living tissues are characterized by an intrinsically mechanochemical interplay
of active physical forces and complex biochemical signaling pathways. Either feature
alone can give rise to complex emergent phenomena, for example, mechanically driven
glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion
instabilities. An important question is how to quantitatively assess the contribution
of these different cues to the large-scale dynamics of biological materials. We
address this in Madin-Darby canine kidney (MDCK) monolayers, considering both
mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling
activity and cellular density as well as a mechanically active tissue rheology
via a self-propelled vertex model. We show that the relative strength of active
migration forces to mechanochemical couplings controls a transition from a uniform
active glass to periodic spatiotemporal waves. We parametrize the model from published
experimental data sets on MDCK monolayers and use it to make new predictions on
the correlation functions of cellular dynamics and the dynamics of topological
defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers
are best described by an intermediary parameter region in which both mechanochemical
couplings and noisy active propulsion have a strong influence on the dynamics.
Finally, we study how tissue rheology and ERK waves produce feedback on one another
and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical
waves at both the local and global levels.
acknowledgement: We thank all members of the Hannezo group for discussions and suggestions,
as well as Sound Wai Phow for technical assistance. This work received funding from
the European Research Council under the EU Horizon 2020 research and innovation
program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and
the Ministry of Education under the Research Centres of Excellence program through
the MBI at NUS.
article_number: '013001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning
and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001
apa: Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between
mechanochemical patterning and glassy dynamics in cellular monolayers. PRX
Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001
chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay
between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.”
PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.
ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers,” PRX Life, vol.
1, no. 1. American Physical Society, 2023.
ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.
mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and
Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001,
American Physical Society, 2023, doi:10.1103/prxlife.1.013001.
short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).
date_created: 2023-09-06T08:30:59Z
date_published: 2023-07-20T00:00:00Z
date_updated: 2023-09-15T06:39:17Z
day: '20'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1103/prxlife.1.013001
ec_funded: 1
file:
- access_level: open_access
checksum: f881d98c89eb9f1aa136d7b781511553
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:30:50Z
date_updated: 2023-09-15T06:30:50Z
file_id: '14335'
file_name: 2023_PRXLife_Boocock.pdf
file_size: 2559520
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:30:50Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: PRX Life
publication_identifier:
issn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Interplay between mechanochemical patterning and glassy dynamics in cellular
monolayers
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: 1
year: '2023'
...
---
_id: '14314'
abstract:
- lang: eng
text: The execution of cognitive functions requires coordinated circuit activity
across different brain areas that involves the associated firing of neuronal assemblies.
Here, we tested the circuit mechanism behind assembly interactions between the
hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording
neuronal populations during a rule-switching task. We identified functionally
coupled CA1-mPFC cells that synchronized their activity beyond that expected from
common spatial coding or oscillatory firing. When such cell pairs fired together,
the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent
theta firing phases, independent of the theta timing of their CA1 counterpart.
These functionally connected CA1-mPFC cells formed interconnected assemblies.
While firing together with their CA1 assembly partners, mPFC cells fired along
specific theta sequences. Our results suggest that upregulated theta oscillatory
firing of mPFC cells can signal transient interactions with specific CA1 assemblies,
thus enabling distributed computations.
acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on
an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS
(grant 607616).
article_number: '113015'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports.
2023;42(9). doi:10.1016/j.celrep.2023.113015
apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations
as a substrate for medial prefrontal-hippocampal assembly interactions. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015
chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari.
“Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly
Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.
ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as
a substrate for medial prefrontal-hippocampal assembly interactions,” Cell
Reports, vol. 42, no. 9. Elsevier, 2023.
ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9),
113015.
mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal
Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier,
2023, doi:10.1016/j.celrep.2023.113015.
short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2023-09-15T07:14:12Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2023.113015
ec_funded: 1
external_id:
pmid:
- '37632747'
file:
- access_level: open_access
checksum: ca77a304fb813c292550b8604b0fb41d
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T07:12:46Z
date_updated: 2023-09-15T07:12:46Z
file_id: '14337'
file_name: 2023_CellPress_Nardin.pdf
file_size: 4879455
relation: main_file
success: 1
file_date_updated: 2023-09-15T07:12:46Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: Inter-and intracellular signalling in schizophrenia
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly
interactions
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: 42
year: '2023'
...
---
_id: '14315'
abstract:
- lang: eng
text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly
demolish the nuclear pore complex. However, for poorly understood reasons, caspases
are also activated during cell differentiation. Here, we show that sublethal activation
of caspases during myogenesis results in the transient proteolysis of four peripheral
Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective,
and we identified in an unbiased manner several classes of cytoplasmic, plasma
membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC
trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic
reticulum stress. Our results suggest that caspases can reversibly modulate nuclear
transport activity, which allows them to function as agents of cell differentiation
and adaptation at sublethal levels.
acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk),
Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital)
for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin
(Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto
and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra
Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing
mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical
Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH),
and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC).
This work was also supported by the Mass Spectrometry Core of the Salk Institute
with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine.
We thank Jolene Diedrich and Antonio Pinto for technical support.'
article_number: RP89066
article_processing_charge: Yes
article_type: original
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation
and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066
apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex
trimming in cell differentiation and endoplasmic reticulum stress. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.89066
chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex
Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife.
eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.
ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12.
eLife Sciences Publications, 2023.
ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.
mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming
in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol.
12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.
short: U.H. Cho, M. Hetzer, ELife 12 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-04T00:00:00Z
date_updated: 2023-09-15T07:07:10Z
day: '04'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.7554/eLife.89066
external_id:
pmid:
- '37665327'
file:
- access_level: open_access
checksum: db24bf3d595507387b48d3799c33e289
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:59:10Z
date_updated: 2023-09-15T06:59:10Z
file_id: '14336'
file_name: 2023_eLife_Cho.pdf
file_size: 3703097
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:59:10Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Caspase-mediated nuclear pore complex trimming in cell differentiation and
endoplasmic reticulum stress
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: 12
year: '2023'
...
---
_id: '14319'
abstract:
- lang: eng
text: "We study multigraphs whose edge-sets are the union of three perfect matchings,
M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6
n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2
f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture
however that if G is bipartite, the same result holds with n - 2 replaced by n
- 1. We give a construction that shows such a result would be tight. We\r\nalso
make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."
acknowledgement: Anastos has received funding from the European Union’s Horizon 2020
research and in-novation programme under the Marie Sk lodowska-Curie grant agreement
No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft
(DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).
article_number: P3.10
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: David
full_name: Fabian, David
last_name: Fabian
- first_name: Alp
full_name: Müyesser, Alp
last_name: Müyesser
- first_name: Tibor
full_name: Szabó, Tibor
last_name: Szabó
citation:
ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein
conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3).
doi:10.37236/11714
apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings
and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of
Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714
chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting
Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.
ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and
the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics,
vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.
ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the
Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics.
30(3), P3.10.
mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture
for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10,
Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.
short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics
30 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2023-09-15T08:12:30Z
day: '28'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11714
ec_funded: 1
external_id:
arxiv:
- '2212.03100'
file:
- access_level: open_access
checksum: 52c46c8cb329f9aaee9ade01525f317b
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T08:02:09Z
date_updated: 2023-09-15T08:02:09Z
file_id: '14338'
file_name: 2023_elecJournCombinatorics_Anastos.pdf
file_size: 247917
relation: main_file
success: 1
file_date_updated: 2023-09-15T08:02:09Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '14318'
abstract:
- lang: eng
text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing
the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider
the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime
T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims
at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem,
the classical and most well-known approach is the cookbook method by Karp (JACM
1994), while other approaches are mostly limited to deriving tail bounds of specific
PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach
for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing
time and random passed sizes observe discrete or (piecewise) uniform distribution
and whose recursive call is either a single procedure call or a divide-and-conquer.
We first establish a theoretical approach via Markov’s inequality, and then instantiate
the theoretical approach with a template-based algorithmic approach via a refined
treatment of exponentiation. Experimental evaluation shows that our algorithmic
approach is capable of deriving tail bounds that are (i) asymptotically tighter
than Karp’s method, (ii) match the best-known manually-derived asymptotic tail
bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor)
than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover,
our algorithmic approach handles all examples (including realistic PRRs such as
QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing
that our approach is efficient in practice."
acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential
theory of reals. The work is partially supported by the National Natural Science
Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt),
the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa
Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic
recurrence relations. In: Computer Aided Verification. Vol 13966. Springer
Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2'
apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated
tail bound analysis for probabilistic recurrence relations. In Computer Aided
Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2'
chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady.
“Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer
Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.
ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound
analysis for probabilistic recurrence relations,” in Computer Aided Verification,
Paris, France, 2023, vol. 13966, pp. 16–39.
ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis
for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer
Aided Verification, LNCS, vol. 13966, 16–39.'
mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence
Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023,
pp. 16–39, doi:10.1007/978-3-031-37709-9_2.
short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 16–39.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-20T08:25:57Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_2
ec_funded: 1
file:
- access_level: open_access
checksum: 42917e086f8c7699f3bccf84f74fe000
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:24:47Z
date_updated: 2023-09-20T08:24:47Z
file_id: '14348'
file_name: 2023_LNCS_Sun.pdf
file_size: 624647
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:24:47Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16-39
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/boyvolcano/PRR
scopus_import: '1'
status: public
title: Automated tail bound analysis for probabilistic recurrence relations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14317'
abstract:
- lang: eng
text: "Markov decision processes can be viewed as transformers of probability distributions.
While this view is useful from a practical standpoint to reason about trajectories
of distributions, basic reachability and safety problems are known to be computationally
intractable (i.e., Skolem-hard) to solve in such models. Further, we show that
even for simple examples of MDPs, strategies for safety objectives over distributions
can require infinite memory and randomization.\r\nIn light of this, we present
a novel overapproximation approach to synthesize strategies in an MDP, such that
a safety objective over the distributions is met. More precisely, we develop a
new framework for template-based synthesis of certificates as affine distributional
and inductive invariants for safety objectives in MDPs. We provide two algorithms
within this framework. One can only synthesize memoryless strategies, but has
relative completeness guarantees, while the other can synthesize general strategies.
The runtime complexity of both algorithms is in PSPACE. We implement these algorithms
and show that they can solve several non-trivial examples."
acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt)
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project
EQuaVE and SERB Matrices grant MTR/2018/00074.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: S.
full_name: Akshay, S.
last_name: Akshay
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers:
Affine invariant synthesis for safety objectives. In: International Conference
on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5'
apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs
as distribution transformers: Affine invariant synthesis for safety objectives.
In International Conference on Computer Aided Verification (Vol. 13966,
pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5'
chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic.
“MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.”
In International Conference on Computer Aided Verification, 13966:86–112.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.'
ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution
transformers: Affine invariant synthesis for safety objectives,” in International
Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966,
pp. 86–112.'
ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution
transformers: Affine invariant synthesis for safety objectives. International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13966, 86–112.'
mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis
for Safety Objectives.” International Conference on Computer Aided Verification,
vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.'
short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International
Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-20T09:04:40Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_5
ec_funded: 1
file:
- access_level: open_access
checksum: f143c8eedf609f20f2aad2eeb496d53f
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:46:43Z
date_updated: 2023-09-20T08:46:43Z
file_id: '14349'
file_name: 2023_LNCS_Akshay.pdf
file_size: 531745
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:46:43Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 86-112
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14316'
abstract:
- lang: eng
text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport.
In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted
to generate distinct transport vesicles at the trans-Golgi network (TGN), and
the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories
for these adaptors. Recently, we showed that vesicle transport from the TGN is
crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p
are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However,
these observations were incompatible with previous studies showing that these
adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall
mechanism responsible for regulation of Vps21p activity remains ambiguous. Here,
we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated
Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired
transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to
the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA
adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and
Ypt32p were found to have partially overlapping functions for recruitment of AP-1
and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors
for Vps21p activation in the TGN–endosome trafficking pathway.
article_number: jcs261448
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Hiroki
full_name: Shimamura, Hiroki
last_name: Shimamura
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct
role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448
apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &
Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p
activation in the TGN-endosome trafficking pathway. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.261448
chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko
Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors
for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of
Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.
ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J.
Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation
in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol.
136, no. 17. The Company of Biologists, 2023.
ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023.
Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 136(17), jcs261448.
mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for
Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell
Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.
short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima,
Journal of Cell Science 136 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-09-20T09:14:15Z
day: '01'
department:
- _id: DaSi
doi: 10.1242/jcs.261448
external_id:
pmid:
- '37539494'
intvolume: ' 136'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.27.534325
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the
TGN-endosome trafficking pathway
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '14320'
abstract:
- lang: eng
text: The development of two-dimensional materials has resulted in a diverse range
of novel, high-quality compounds with increasing complexity. A key requirement
for a comprehensive quantitative theory is the accurate determination of these
materials' band structure parameters. However, this task is challenging due to
the intricate band structures and the indirect nature of experimental probes.
In this work, we introduce a general framework to derive band structure parameters
from experimental data using deep neural networks. We applied our method to the
penetration field capacitance measurement of trilayer graphene, an effective probe
of its density of states. First, we demonstrate that a trained deep network gives
accurate predictions for the penetration field capacitance as a function of tight-binding
parameters. Next, we use the fast and accurate predictions from the trained network
to automatically determine tight-binding parameters directly from experimental
data, with extracted parameters being in a good agreement with values in the literature.
We conclude by discussing potential applications of our method to other materials
and experimental techniques beyond penetration field capacitance.
acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy
under award DE-SC0020043, and additional support from the Gordon and Betty Moore
Foundation under award GBMF9471 for group operations.
article_number: '125411'
article_processing_charge: No
article_type: original
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alexander A.
full_name: Zibrov, Alexander A.
last_name: Zibrov
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction
of band structure parameters from density of states: A case study on trilayer
graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411'
apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn,
M. (2023). Deep learning extraction of band structure parameters from density
of states: A case study on trilayer graphene. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.108.125411'
chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young,
and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from
Density of States: A Case Study on Trilayer Graphene.” Physical Review B.
American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.'
ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn,
“Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12.
American Physical Society, 2023.'
ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning
extraction of band structure parameters from density of states: A case study on
trilayer graphene. Physical Review B. 108(12), 125411.'
mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters
from Density of States: A Case Study on Trilayer Graphene.” Physical Review
B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.'
short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical
Review B 108 (2023).
date_created: 2023-09-12T07:12:12Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-09-20T09:38:24Z
day: '15'
department:
- _id: MaSe
- _id: ChLa
- _id: MiLe
doi: 10.1103/physrevb.108.125411
external_id:
arxiv:
- '2210.06310'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06310
month: '09'
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: 'Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '12732'
abstract:
- lang: eng
text: "Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize,
provide a fascinating research direction both for fundamental reasons and for
application in state of the art quantum devices.\r\nGoing beyond the description
of statistical mechanics, ergodicity breaking yields a new paradigm in quantum
many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn
this Thesis, we address different open questions in the field, focusing on disorder-induced
many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained
models.\r\nIn particular, we contribute to the debate about transport in kinetically
constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry
breaking in a family of quantum East models.\r\nUsing tensor network techniques,
we analyze the dynamics of large MBL systems beyond the limit of exact numerical
methods.\r\nIn this setting, we approach the debated topic of the coexistence
of localized and thermal eigenstates separated by energy thresholds known as many-body
mobility edges.\r\nInspired by recent experiments, our work further investigates
the localization of a small bath induced by the coupling to a large localized
chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce
a family of particle-conserving kinetically constrained models, inspired by the
quantum East model.\r\nThe system we study features strong inversion-symmetry
breaking, due to the nature of the correlated hopping.\r\nWe show that these models
host so-called quantum Hilbert space fragmentation, consisting of disconnected
subsectors in an entangled basis, and further provide an analytical description
of this phenomenon.\r\nWe further probe its effect on dynamics of simple product
states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics
within the largest subsector reveals an anomalous transient superdiffusive behavior
crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests
that particle conserving constrained models with inversion-symmetry breaking realize
new universality classes of dynamics and invite their further theoretical and
experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to
design a model with many-body mobility edges in particle density.\r\nThis feature
allows to study the dynamics of localized and thermal states in large systems
beyond the limitations of previous studies.\r\nThe time-evolution shows typical
signatures of localization at small densities, replaced by thermal behavior at
larger densities.\r\nOur results provide evidence in favor of the stability of
many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo
support our findings, we probe the mechanism proposed as a cause of delocalization
in many-body localized systems with mobility edges suggesting its ineffectiveness
in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the
topic of many-body localization proximity effect.\r\nWe study a model inspired
by recent experiments, featuring Anderson localized coupled to a small bath of
free hard-core bosons.\r\nThe interaction among the two particle species results
in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur
simulations show convincing evidence of many-body localization proximity effect
when the bath is composed by a single free particle and interactions are strong.\r\nWe
furthter observe an anomalous entanglement dynamics, which we explain through
a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of
large systems, providing supplementary evidence in favor of our findings."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
citation:
ama: Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum
many-body systems. 2023. doi:10.15479/at:ista:12732
apa: Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732
chicago: Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:12732.
ieee: P. Brighi, “Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems,” Institute of Science and Technology Austria, 2023.
ista: Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems. Institute of Science and Technology Austria.
mla: Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:12732.
short: P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-17T13:30:48Z
date_published: 2023-03-21T00:00:00Z
date_updated: 2023-09-20T10:44:12Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaSe
doi: 10.15479/at:ista:12732
ec_funded: 1
file:
- access_level: closed
checksum: 5d2de651ef9449c1b8dc27148ca74777
content_type: application/zip
creator: pbrighi
date_created: 2023-03-23T16:42:56Z
date_updated: 2023-03-23T16:42:56Z
file_id: '12753'
file_name: Thesis_sub_PBrighi.zip
file_size: 42167561
relation: source_file
- access_level: open_access
checksum: 7caa153d4a5b0873a79358787d2dfe1e
content_type: application/pdf
creator: pbrighi
date_created: 2023-03-23T16:43:14Z
date_updated: 2023-03-23T16:43:14Z
file_id: '12754'
file_name: Thesis_PBrighi.pdf
file_size: 13977000
relation: main_file
success: 1
file_date_updated: 2023-03-23T16:43:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: None
page: '158'
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11470'
relation: part_of_dissertation
status: public
- id: '8308'
relation: part_of_dissertation
status: public
- id: '11469'
relation: part_of_dissertation
status: public
- id: '12750'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
title: Ergodicity breaking in disordered and kinetically constrained quantum many-body
systems
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: '14334'
abstract:
- lang: eng
text: Quantum kinetically constrained models have recently attracted significant
attention due to their anomalous dynamics and thermalization. In this work, we
introduce a hitherto unexplored family of kinetically constrained models featuring
conserved particle number and strong inversion-symmetry breaking due to facilitated
hopping. We demonstrate that these models provide a generic example of so-called
quantum Hilbert space fragmentation, that is manifested in disconnected sectors
in the Hilbert space that are not apparent in the computational basis. Quantum
Hilbert space fragmentation leads to an exponential in system size number of eigenstates
with exactly zero entanglement entropy across several bipartite cuts. These eigenstates
can be probed dynamically using quenches from simple initial product states. In
addition, we study the particle spreading under unitary dynamics launched from
the domain wall state, and find faster than diffusive dynamics at high particle
densities, that crosses over into logarithmically slow relaxation at smaller densities.
Using a classically simulable cellular automaton, we reproduce the logarithmic
dynamics observed in the quantum case. Our work suggests that particle conserving
constrained models with inversion symmetry breaking realize so far unexplored
dynamical behavior and invite their further theoretical and experimental studies.
acknowledgement: "We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry
Abanin for useful\r\ndiscussions.The authors acknowledge support by the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger
International\r\nInstitute for Mathematics and Physics (ESI)."
article_number: '093'
article_processing_charge: No
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
orcid: 0000-0003-0038-7068
- 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, Serbyn M. Hilbert space fragmentation and slow dynamics
in particle-conserving quantum East models. SciPost Physics. 2023;15(3).
doi:10.21468/scipostphys.15.3.093
apa: Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation
and slow dynamics in particle-conserving quantum East models. SciPost Physics.
SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093
chicago: Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation
and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics.
SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.
ieee: P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models,” SciPost Physics,
vol. 15, no. 3. SciPost Foundation, 2023.
ista: Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.
mla: Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving
Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation,
2023, doi:10.21468/scipostphys.15.3.093.
short: P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).
date_created: 2023-09-14T13:08:23Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2023-09-20T10:46:29Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.15.3.093
ec_funded: 1
external_id:
arxiv:
- '2210.15607'
file:
- access_level: open_access
checksum: 4cef6a8021f6b6c47ab2f2f2b1387ac2
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:46:10Z
date_updated: 2023-09-20T10:46:10Z
file_id: '14350'
file_name: 2023_SciPostPhysics_Brighi.pdf
file_size: 4866506
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:46:10Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
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: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
record:
- id: '12750'
relation: earlier_version
status: public
status: public
title: Hilbert space fragmentation and slow dynamics in particle-conserving quantum
East models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- 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: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2023-09-20T09:48:12Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Achiral dipoles on a ferromagnet can affect its magnetization direction
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: 159
year: '2023'
...
---
_id: '14342'
abstract:
- lang: eng
text: We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared
frequency range that avoids using sophisticated infrared detectors. Our approach
is based on using a near-infrared probe beam which interacts with a mid-IR beam
via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring
XPM-induced spectral modifications in the probe beam and comparing the experimental
data with simulation results, we extract the value for the non-degenerate Kerr
index. Finally, in order to obtain the value of degenerate mid-IR Kerr index,
we use the well-established two-band formalism of Sheik-Bahae et al., which is
shown to become particularly simple in the limit of low frequencies. The proposed
technique is complementary to the conventional techniques, such as z-scan, and
has the advantage of not requiring any mid-infrared detectors.
acknowledgement: The work was supported by IST Austria. The authors would like to
gratefully acknowledge the help and assistance of Professor John M. Dudley.
article_number: '091104'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9).
doi:10.1063/5.0161713
apa: Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation
via cross-phase modulation with a near-infrared probe beam. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0161713
chicago: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.
ieee: D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam,” Applied Physics Letters, vol.
123, no. 9. AIP Publishing, 2023.
ista: Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.
mla: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.
short: D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).
date_created: 2023-09-17T22:01:09Z
date_published: 2023-08-28T00:00:00Z
date_updated: 2023-09-20T11:50:06Z
day: '28'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1063/5.0161713
external_id:
arxiv:
- '2306.09043'
file:
- access_level: open_access
checksum: 89a1b604d58b209fec66c6b6f919ac98
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T11:36:16Z
date_updated: 2023-09-20T11:36:16Z
file_id: '14353'
file_name: 2023_ApplPhysLetter_Lorenc.pdf
file_size: 1486715
relation: main_file
success: 1
file_date_updated: 2023-09-20T11:36:16Z
has_accepted_license: '1'
intvolume: ' 123'
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared
probe beam
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: 123
year: '2023'
...
---
_id: '14341'
abstract:
- lang: eng
text: Flows through pipes and channels are, in practice, almost always turbulent,
and the multiscale eddying motion is responsible for a major part of the encountered
friction losses and pumping costs1. Conversely, for pulsatile flows, in particular
for aortic blood flow, turbulence levels remain low despite relatively large peak
velocities. For aortic blood flow, high turbulence levels are intolerable as they
would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that
turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile
mode that incorporates all the key features of the cardiac waveform. At Reynolds
numbers comparable to those of aortic blood flow, turbulence is largely inhibited,
whereas at much higher speeds, the turbulent drag is reduced by more than 25%.
This specific operation mode is more efficient when compared with steady driving,
which is the present situation for virtually all fluid transport processes ranging
from heating circuits to water, gas and oil pipelines.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: We acknowledge the assistance of the Miba machine shop and the team
of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported
by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant
no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by
cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74.
doi:10.1038/s41586-023-06399-5
apa: Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence
suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer
Nature. https://doi.org/10.1038/s41586-023-06399-5
chicago: Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence
Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.
ieee: D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no.
7977. Springer Nature, pp. 71–74, 2023.
ista: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.
mla: Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired
Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023,
pp. 71–74, doi:10.1038/s41586-023-06399-5.
short: D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.
date_created: 2023-09-17T22:01:09Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2023-09-20T12:10:22Z
day: '07'
department:
- _id: BjHo
doi: 10.1038/s41586-023-06399-5
external_id:
pmid:
- '37673988'
intvolume: ' 621'
issue: '7977'
language:
- iso: eng
month: '09'
oa_version: None
page: 71-74
pmid: 1
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow of Newtonian and complex fluids
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://www.ista.ac.at/en/news/pumping-like-the-heart/
scopus_import: '1'
status: public
title: Turbulence suppression by cardiac-cycle-inspired driving of pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 621
year: '2023'
...
---
_id: '13120'
abstract:
- lang: eng
text: 'We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant.
We defined basic notions of rewrite rules and of words derived by a grammar, and
used grammars to show closure of the class of type-0 languages under four operations:
union, reversal, concatenation, and the Kleene star. The literature mostly focuses
on Turing machine arguments, which are possibly more difficult to formalize. For
the Kleene star, we could not follow the literature and came up with our own grammar-based
construction.'
acknowledgement: "Jasmin Blanchette: This research has received funding from the Netherlands
Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No.
016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making
this collaboration possible. We\r\nthank Václav Končický for discussing ideas about
the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano
Testa for their small yet very valuable contributions to our code. We thank Eric
Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting
textual improvements. We thank the anonymous reviewers for very helpful comments.
Finally, we thank the Lean community for helping us with various technical issues
and answering many questions. "
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: No
author:
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
- first_name: Jasmin
full_name: Blanchette, Jasmin
last_name: Blanchette
citation:
ama: 'Dvorak M, Blanchette J. Closure properties of general grammars - formally
verified. In: 14th International Conference on Interactive Theorem Proving.
Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15'
apa: 'Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars
- formally verified. In 14th International Conference on Interactive Theorem
Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15'
chicago: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars
- Formally Verified.” In 14th International Conference on Interactive Theorem
Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
https://doi.org/10.4230/LIPIcs.ITP.2023.15.
ieee: M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally
verified,” in 14th International Conference on Interactive Theorem Proving,
Bialystok, Poland, 2023, vol. 268.
ista: 'Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally
verified. 14th International Conference on Interactive Theorem Proving. ITP: International
Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.'
mla: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars
- Formally Verified.” 14th International Conference on Interactive Theorem
Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ITP.2023.15.
short: M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive
Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-08-04
location: Bialystok, Poland
name: 'ITP: International Conference on Interactive Theorem Proving'
start_date: 2023-07-31
date_created: 2023-06-05T07:29:05Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-09-25T11:04:29Z
day: '27'
ddc:
- '000'
department:
- _id: GradSch
- _id: VlKo
doi: 10.4230/LIPIcs.ITP.2023.15
external_id:
arxiv:
- '2302.06420'
file:
- access_level: open_access
checksum: 773a0197f05b67feaa6cb1e17ec3642d
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T11:55:43Z
date_updated: 2023-08-07T11:55:43Z
file_id: '13982'
file_name: 2023_LIPIcS_Dvorak.pdf
file_size: 715976
relation: main_file
success: 1
file_date_updated: 2023-08-07T11:55:43Z
has_accepted_license: '1'
intvolume: ' 268'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 14th International Conference on Interactive Theorem Proving
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772846'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/madvorak/grammars/tree/publish
scopus_import: '1'
status: public
title: Closure properties of general grammars - formally verified
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 268
year: '2023'
...
---
_id: '13969'
abstract:
- lang: eng
text: "Bundling crossings is a strategy which can enhance the readability\r\nof
graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany
two edges have at most one common point which can be a common vertex or a\r\ncrossing.
Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation
of the bundled crossing number of a good drawing with no toothed\r\nhole. In general
the number of toothed holes has to be added to the 8-approximation.\r\nIn the
special case of circular drawings the approximation factor is 8, this improves\r\nupon
the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation
factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce.
We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe
pseudosegments is bipartite and has no toothed hole."
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1. An extended abstract of this paper has been published in
the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.
article_processing_charge: Yes
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: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal
of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629
apa: Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled
crossing number. Journal of Graph Algorithms and Applications. Brown University.
https://doi.org/10.7155/jgaa.00629
chicago: Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” Journal of Graph Algorithms and Applications. Brown University,
2023. https://doi.org/10.7155/jgaa.00629.
ieee: A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,”
Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University,
pp. 433–457, 2023.
ista: Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number.
Journal of Graph Algorithms and Applications. 27(6), 433–457.
mla: Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6,
Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629.
short: A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications
27 (2023) 433–457.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-09-25T10:56:10Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.7155/jgaa.00629
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
file:
- access_level: open_access
checksum: 9c30d2b8e324cc1c904f2aeec92013a3
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T08:00:48Z
date_updated: 2023-08-07T08:00:48Z
file_id: '13979'
file_name: 2023_JourGraphAlgorithms_Arroyo.pdf
file_size: 865774
relation: main_file
success: 1
file_date_updated: 2023-08-07T08:00:48Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 433-457
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Graph Algorithms and Applications
publication_identifier:
issn:
- 1526-1719
publication_status: published
publisher: Brown University
quality_controlled: '1'
related_material:
record:
- id: '11185'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Approximating the bundled crossing number
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: 27
year: '2023'
...
---
_id: '14344'
abstract:
- lang: eng
text: We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in
two different settings. In the first one, G is given to us in the form of randomly
ordered adjacency lists while in the second one, we are given the adjacency matrix
of G. In each of the two settings we derive a deterministic algorithm that w.h.p.
either finds a Hamilton cycle or returns a certificate that such a cycle does
not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively,
each being best possible in its own setting.
article_processing_charge: No
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: 'Anastos M. Fast algorithms for solving the Hamilton cycle problem with high
probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88'
apa: 'Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem
with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88'
chicago: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem
with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/1.9781611977554.ch88.
ieee: M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high
probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Florence, Italy, 2023, vol. 2023, pp. 2286–2323.
ista: 'Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with
high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.'
mla: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with
High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023,
pp. 2286–323, doi:10.1137/1.9781611977554.ch88.
short: M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
date_created: 2023-09-17T22:01:10Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-25T09:13:41Z
day: '01'
department:
- _id: MaKw
doi: 10.1137/1.9781611977554.ch88
external_id:
arxiv:
- '2111.14759'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.14759
month: '01'
oa: 1
oa_version: Preprint
page: 2286-2323
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast algorithms for solving the Hamilton cycle problem with high probability
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '12710'
abstract:
- lang: eng
text: Surface curvature both emerges from, and influences the behavior of, living
objects at length scales ranging from cell membranes to single cells to tissues
and organs. The relevance of surface curvature in biology is supported by numerous
experimental and theoretical investigations in recent years. In this review, first,
a brief introduction to the key ideas of surface curvature in the context of biological
systems is given and the challenges that arise when measuring surface curvature
are discussed. Giving an overview of the emergence of curvature in biological
systems, its significance at different length scales becomes apparent. On the
other hand, summarizing current findings also shows that both single cells and
entire cell sheets, tissues or organisms respond to curvature by modulating their
shape and their migration behavior. Finally, the interplay between the distribution
of morphogens or micro-organisms and the emergence of curvature across length
scales is addressed with examples demonstrating these key mechanistic principles
of morphogenesis. Overall, this review highlights that curved interfaces are not
merely a passive by-product of the chemical, biological, and mechanical processes
but that curvature acts also as a signal that co-determines these processes.
acknowledgement: B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F.
acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through
IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from
Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD.
A.S. acknowledges that this work was partially supported by the ATTRACT Investigator
Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research
Fund. The author thanks Gerardo Ceada for his help in the graphical representations.
N.A.K. acknowledges support from the European Research Council (grant 851960) and
the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands
Organization for Scientific Research (024.003.013). M.B.A. acknowledges support
from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project
“Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through
project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft
(DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation
(PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.
article_number: '2206110'
article_processing_charge: No
article_type: review
author:
- first_name: Barbara
full_name: Schamberger, Barbara
last_name: Schamberger
- first_name: Ricardo
full_name: Ziege, Ricardo
last_name: Ziege
- first_name: Karine
full_name: Anselme, Karine
last_name: Anselme
- first_name: Martine
full_name: Ben Amar, Martine
last_name: Ben Amar
- first_name: Michał
full_name: Bykowski, Michał
last_name: Bykowski
- first_name: André P.G.
full_name: Castro, André P.G.
last_name: Castro
- first_name: Amaia
full_name: Cipitria, Amaia
last_name: Cipitria
- first_name: Rhoslyn A.
full_name: Coles, Rhoslyn A.
last_name: Coles
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Michaela
full_name: Eder, Michaela
last_name: Eder
- first_name: Sebastian
full_name: Ehrig, Sebastian
last_name: Ehrig
- first_name: Luis M.
full_name: Escudero, Luis M.
last_name: Escudero
- first_name: Myfanwy E.
full_name: Evans, Myfanwy E.
last_name: Evans
- first_name: Paulo R.
full_name: Fernandes, Paulo R.
last_name: Fernandes
- first_name: Peter
full_name: Fratzl, Peter
last_name: Fratzl
- first_name: Liesbet
full_name: Geris, Liesbet
last_name: Geris
- first_name: Notburga
full_name: Gierlinger, Notburga
last_name: Gierlinger
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Aleš
full_name: Iglič, Aleš
last_name: Iglič
- first_name: Jacob J.K.
full_name: Kirkensgaard, Jacob J.K.
last_name: Kirkensgaard
- first_name: Philip
full_name: Kollmannsberger, Philip
last_name: Kollmannsberger
- first_name: Łucja
full_name: Kowalewska, Łucja
last_name: Kowalewska
- first_name: Nicholas A.
full_name: Kurniawan, Nicholas A.
last_name: Kurniawan
- first_name: Ioannis
full_name: Papantoniou, Ioannis
last_name: Papantoniou
- first_name: Laurent
full_name: Pieuchot, Laurent
last_name: Pieuchot
- first_name: Tiago H.V.
full_name: Pires, Tiago H.V.
last_name: Pires
- first_name: Lars D.
full_name: Renner, Lars D.
last_name: Renner
- first_name: Andrew O.
full_name: Sageman-Furnas, Andrew O.
last_name: Sageman-Furnas
- first_name: Gerd E.
full_name: Schröder-Turk, Gerd E.
last_name: Schröder-Turk
- first_name: Anupam
full_name: Sengupta, Anupam
last_name: Sengupta
- first_name: Vikas R.
full_name: Sharma, Vikas R.
last_name: Sharma
- first_name: Antonio
full_name: Tagua, Antonio
last_name: Tagua
- first_name: Caterina
full_name: Tomba, Caterina
last_name: Tomba
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Sarah L.
full_name: Waters, Sarah L.
last_name: Waters
- first_name: Edwina F.
full_name: Yeo, Edwina F.
last_name: Yeo
- first_name: Andreas
full_name: Roschger, Andreas
last_name: Roschger
- first_name: Cécile M.
full_name: Bidan, Cécile M.
last_name: Bidan
- first_name: John W.C.
full_name: Dunlop, John W.C.
last_name: Dunlop
citation:
ama: 'Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems:
Its quantification, emergence, and implications across the scales. Advanced
Materials. 2023;35(13). doi:10.1002/adma.202206110'
apa: 'Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro,
A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification,
emergence, and implications across the scales. Advanced Materials. Wiley.
https://doi.org/10.1002/adma.202206110'
chicago: 'Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar,
Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological
Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced
Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.'
ieee: 'B. Schamberger et al., “Curvature in biological systems: Its quantification,
emergence, and implications across the scales,” Advanced Materials, vol.
35, no. 13. Wiley, 2023.'
ista: 'Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria
A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl
P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger
P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD,
Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C,
Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature
in biological systems: Its quantification, emergence, and implications across
the scales. Advanced Materials. 35(13), 2206110.'
mla: 'Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification,
Emergence, and Implications across the Scales.” Advanced Materials, vol.
35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.'
short: B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro,
A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans,
P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K.
Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou,
L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk,
A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo,
A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).
date_created: 2023-03-05T23:01:06Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2023-09-26T10:56:46Z
day: '29'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1002/adma.202206110
external_id:
isi:
- '000941068900001'
pmid:
- '36461812'
file:
- access_level: open_access
checksum: 5c04d68130e97a0ecd1ca27fbc15a246
content_type: application/pdf
creator: dernst
date_created: 2023-09-26T10:51:56Z
date_updated: 2023-09-26T10:51:56Z
file_id: '14373'
file_name: 2023_AdvancedMaterials_Schamberger.pdf
file_size: 2898063
relation: main_file
success: 1
file_date_updated: 2023-09-26T10:51:56Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Curvature in biological systems: Its quantification, emergence, and implications
across the scales'
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: '13340'
abstract:
- lang: eng
text: Photoisomerization of azobenzenes from their stable E isomer to the metastable
Z state is the basis of numerous applications of these molecules. However, this
reaction typically requires ultraviolet light, which limits applicability. In
this study, we introduce disequilibration by sensitization under confinement (DESC),
a supramolecular approach to induce the E-to-Z isomerization by using light of
a desired color, including red. DESC relies on a combination of a macrocyclic
host and a photosensitizer, which act together to selectively bind and sensitize
E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is
expelled from the host, which can then convert additional E-azobenzenes to the
Z state. In this way, the host–photosensitizer complex converts photon energy
into chemical energy in the form of out-of-equilibrium photostationary states,
including ones that cannot be accessed through direct photoexcitation.
acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research
and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223
(A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)],
the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.),
Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant
340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s
PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1
(M.J.F.)].
article_processing_charge: No
article_type: original
author:
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Jonathan R.
full_name: Church, Jonathan R.
last_name: Church
- first_name: Tero-Petri
full_name: Ruoko, Tero-Petri
last_name: Ruoko
- first_name: Nikita
full_name: Durandin, Nikita
last_name: Durandin
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Maren
full_name: Weissenfels, Maren
last_name: Weissenfels
- first_name: Moran
full_name: Feller, Moran
last_name: Feller
- first_name: Miri
full_name: Kazes, Miri
last_name: Kazes
- first_name: Veniamin A.
full_name: Borin, Veniamin A.
last_name: Borin
- first_name: Magdalena
full_name: Odaybat, Magdalena
last_name: Odaybat
- first_name: Rishir
full_name: Kalepu, Rishir
last_name: Kalepu
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Dan
full_name: Oron, Dan
last_name: Oron
- first_name: Matthew J.
full_name: Fuchter, Matthew J.
last_name: Fuchter
- first_name: Arri
full_name: Priimagi, Arri
last_name: Priimagi
- first_name: Igor
full_name: Schapiro, Igor
last_name: Schapiro
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light
sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059
apa: Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels,
M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization
under confinement. Science. American Association for the Advancement of
Science. https://doi.org/10.1126/science.adh9059
chicago: Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał
J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes
by Visible-Light Sensitization under Confinement.” Science. American Association
for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059.
ieee: J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization
under confinement,” Science, vol. 381, no. 6664. American Association for
the Advancement of Science, pp. 1357–1363, 2023.
ista: Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller
M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ,
Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light
sensitization under confinement. Science. 381(6664), 1357–1363.
mla: Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization
under Confinement.” Science, vol. 381, no. 6664, American Association for
the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.
short: J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels,
M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron,
M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.
date_created: 2023-08-01T08:26:15Z
date_published: 2023-09-22T00:00:00Z
date_updated: 2023-10-03T08:11:26Z
day: '22'
department:
- _id: RaKl
doi: 10.1126/science.adh9059
intvolume: ' 381'
issue: '6664'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv-2023-gq2h0
month: '09'
oa: 1
oa_version: Preprint
page: 1357-1363
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disequilibrating azoarenes by visible-light sensitization under confinement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '12705'
abstract:
- lang: eng
text: The elasticity of disordered and polydisperse polymer networks is a fundamental
problem of soft matter physics that is still open. Here, we self-assemble polymer
networks via simulations of a mixture of bivalent and tri- or tetravalent patchy
particles, which result in an exponential strand length distribution analogous
to that of experimental randomly cross-linked systems. After assembly, the network
connectivity and topology are frozen and the resulting system is characterized.
We find that the fractal structure of the network depends on the number density
at which the assembly has been carried out, but that systems with the same mean
valence and same assembly density have the same structural properties. Moreover,
we compute the long-time limit of the mean-squared displacement, also known as
the (squared) localization length, of the cross-links and of the middle monomers
of the strands, showing that the dynamics of long strands is well described by
the tube model. Finally, we find a relation connecting these two localization
lengths at high density and connect the cross-link localization length to the
shear modulus of the system.
acknowledgement: We thank Michael Lang for helpful discussions. We acknowledge financial
support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC)
and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir”
French Government program, managed by the French National Research Agency (ANR).
W.K. is a senior member of the Institut Universitaire de France.
article_number: '074905'
article_processing_charge: No
article_type: original
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Andrea
full_name: Ninarello, Andrea
last_name: Ninarello
- first_name: José
full_name: Ruiz-Franco, José
last_name: Ruiz-Franco
- first_name: Virginie
full_name: Hugouvieux, Virginie
last_name: Hugouvieux
- first_name: Emanuela
full_name: Zaccarelli, Emanuela
last_name: Zaccarelli
- first_name: Cristian
full_name: Micheletti, Cristian
last_name: Micheletti
- first_name: Walter
full_name: Kob, Walter
last_name: Kob
- first_name: Lorenzo
full_name: Rovigatti, Lorenzo
last_name: Rovigatti
citation:
ama: Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of
model disordered, polydisperse, and defect-free polymer networks. Journal of
Chemical Physics. 2023;158(7). doi:10.1063/5.0134271
apa: Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli,
E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model
disordered, polydisperse, and defect-free polymer networks. Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271
chicago: Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux,
Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure
and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.”
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.
ieee: V. Sorichetti et al., “Structure and elasticity of model disordered,
polydisperse, and defect-free polymer networks,” Journal of Chemical Physics,
vol. 158, no. 7. American Institute of Physics, 2023.
ista: Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti
C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse,
and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.
mla: Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered,
Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics,
vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.
short: V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli,
C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).
date_created: 2023-03-05T23:01:05Z
date_published: 2023-02-21T00:00:00Z
date_updated: 2023-10-03T11:31:51Z
day: '21'
department:
- _id: AnSa
doi: 10.1063/5.0134271
external_id:
arxiv:
- '2211.04810'
isi:
- '000936943800002'
pmid:
- '36813705'
intvolume: ' 158'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04810
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and elasticity of model disordered, polydisperse, and defect-free
polymer networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 158
year: '2023'
...
---
_id: '12738'
abstract:
- lang: eng
text: We study turn-based stochastic zero-sum games with lexicographic preferences
over objectives. Stochastic games are standard models in control, verification,
and synthesis of stochastic reactive systems that exhibit both randomness as well
as controllable and adversarial non-determinism. Lexicographic order allows one
to consider multiple objectives with a strict preference order. To the best of
our knowledge, stochastic games with lexicographic objectives have not been studied
before. For a mixture of reachability and safety objectives, we show that deterministic
lexicographically optimal strategies exist and memory is only required to remember
the already satisfied and violated objectives. For a constant number of objectives,
we show that the relevant decision problem is in NP∩coNP, matching the current
known bound for single objectives; and in general the decision problem is PSPACE-hard
and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes
the lexicographically optimal strategies via a reduction to the computation of
optimal strategies in a sequence of single-objectives games. For omega-regular
objectives, we restrict our analysis to one-player games, also known as Markov
decision processes. We show that lexicographically optimal strategies exist and
need either randomization or finite memory. We present an algorithm that solves
the relevant decision problem in polynomial time. We have implemented our algorithms
and report experimental results on various case studies.
acknowledgement: Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG
2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant
agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC
CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project
ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical
Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic
Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open
Access funding enabled and organized by Projekt DEAL.
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Stefanie
full_name: Mohr, Stefanie
last_name: Mohr
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
- first_name: Tobias
full_name: Winkler, Tobias
last_name: Winkler
citation:
ama: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with
lexicographic objectives. Formal Methods in System Design. 2023. doi:10.1007/s10703-023-00411-4
apa: Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2023).
Stochastic games with lexicographic objectives. Formal Methods in System Design.
Springer Nature. https://doi.org/10.1007/s10703-023-00411-4
chicago: Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger,
and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal
Methods in System Design. Springer Nature, 2023. https://doi.org/10.1007/s10703-023-00411-4.
ieee: K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic
games with lexicographic objectives,” Formal Methods in System Design.
Springer Nature, 2023.
ista: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic
games with lexicographic objectives. Formal Methods in System Design.
mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.”
Formal Methods in System Design, Springer Nature, 2023, doi:10.1007/s10703-023-00411-4.
short: K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods
in System Design (2023).
date_created: 2023-03-19T23:00:59Z
date_published: 2023-03-08T00:00:00Z
date_updated: 2023-10-03T11:36:13Z
day: '08'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s10703-023-00411-4
ec_funded: 1
external_id:
isi:
- '000946174300001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10703-023-00411-4
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Formal Methods in System Design
publication_identifier:
eissn:
- 1572-8102
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8272'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Stochastic games with lexicographic objectives
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
year: '2023'
...
---
_id: '14279'
abstract:
- lang: eng
text: "The zip file includes source data used in the manuscript \"CCR7 acts as both
a sensor and a sink for CCL19 to coordinate collective leukocyte migration\",
as well as a representative Jupyter notebook to reproduce the main figures. Please
see the preprint on bioRxiv and the DOI link there to access the final published
version. Note the title change between the preprint and the published manuscript.\r\nA
sample script for particle-based simulations of collective chemotaxis by self-generated
gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb)
to generate exemplary cell trajectories. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt."
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960
apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023.
https://doi.org/10.5281/ZENODO.8133960.
ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and
a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.
ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.
mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo,
2023, doi:10.5281/ZENODO.8133960.
short: M.C. Ucar, (2023).
date_created: 2023-09-06T08:39:25Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-10-03T11:42:58Z
day: '11'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.8133960
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133960
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14274'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration"
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: '10405'
abstract:
- lang: eng
text: 'We consider large non-Hermitian random matrices X with complex, independent,
identically distributed centred entries and show that the linear statistics of
their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives.
Previously this result was known only for a few special cases; either the test
functions were required to be analytic [72], or the distribution of the matrix
elements needed to be Gaussian [73], or at least match the Gaussian up to the
first four moments [82, 56]. We find the exact dependence of the limiting variance
on the fourth cumulant that was not known before. The proof relies on two novel
ingredients: (i) a local law for a product of two resolvents of the Hermitisation
of X with different spectral parameters and (ii) a coupling of several weakly
dependent Dyson Brownian motions. These methods are also the key inputs for our
analogous results on the linear eigenvalue statistics of real matrices X that
are presented in the companion paper [32]. '
acknowledgement: L.E. would like to thank Nathanaël Berestycki and D.S.would like
to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and
L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding
from the European Union’s Horizon 2020 research and in-novation programme under
the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max
Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.
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. Central limit theorem for linear eigenvalue
statistics of non-Hermitian random matrices. Communications on Pure and Applied
Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem
for linear eigenvalue statistics of non-Hermitian random matrices. Communications
on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit
Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications
on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear
eigenvalue statistics of non-Hermitian random matrices,” Communications on
Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear
eigenvalue statistics of non-Hermitian random matrices. Communications on Pure
and Applied Mathematics. 76(5), 946–1034.
mla: Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics
of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics,
vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied
Mathematics 76 (2023) 946–1034.
date_created: 2021-12-05T23:01:41Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T09:22:55Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1002/cpa.22028
ec_funded: 1
external_id:
arxiv:
- '1912.04100'
isi:
- '000724652500001'
file:
- access_level: open_access
checksum: 8346bc2642afb4ccb7f38979f41df5d9
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:21:48Z
date_updated: 2023-10-04T09:21:48Z
file_id: '14388'
file_name: 2023_CommPureMathematics_Cipolloni.pdf
file_size: 803440
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:21:48Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 946-1034
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Communications on Pure and Applied Mathematics
publication_identifier:
eissn:
- 1097-0312
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Central limit theorem for linear eigenvalue statistics of non-Hermitian random
matrices
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: 76
year: '2023'
...
---
_id: '10770'
abstract:
- lang: eng
text: Mathematical models often aim to describe a complicated mechanism in a cohesive
and simple manner. However, reaching perfect balance between being simple enough
or overly simplistic is a challenging task. Frequently, game-theoretic models
have an underlying assumption that players, whenever they choose to execute a
specific action, do so perfectly. In fact, it is rare that action execution perfectly
coincides with intentions of individuals, giving rise to behavioural mistakes.
The concept of incompetence of players was suggested to address this issue in
game-theoretic settings. Under the assumption of incompetence, players have non-zero
probabilities of executing a different strategy from the one they chose, leading
to stochastic outcomes of the interactions. In this article, we survey results
related to the concept of incompetence in classic as well as evolutionary game
theory and provide several new results. We also suggest future extensions of the
model and argue why it is important to take into account behavioural mistakes
when analysing interactions among players in both economic and biological settings.
acknowledgement: "The authors would like to acknowledge stimulating email discussions
with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also
thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors
would like to acknowledge partial support from the Australian Research Council under
the Discovery grant DP180101602 and support by the European Union’s Horizon 2020
research and innovation program under the Marie Sklodowska-Curie Grant Agreement
#754411."
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Graham, Thomas
last_name: Graham
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Jerzy A.
full_name: Filar, Jerzy A.
last_name: Filar
citation:
ama: Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games
with incompetent players. Dynamic Games and Applications. 2023;13:231-264.
doi:10.1007/s13235-022-00425-3
apa: Graham, T., Kleshnina, M., & Filar, J. A. (2023). Where do mistakes lead?
A survey of games with incompetent players. Dynamic Games and Applications.
Springer Nature. https://doi.org/10.1007/s13235-022-00425-3
chicago: Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes
Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications.
Springer Nature, 2023. https://doi.org/10.1007/s13235-022-00425-3.
ieee: T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey
of games with incompetent players,” Dynamic Games and Applications, vol.
13. Springer Nature, pp. 231–264, 2023.
ista: Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of
games with incompetent players. Dynamic Games and Applications. 13, 231–264.
mla: Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent
Players.” Dynamic Games and Applications, vol. 13, Springer Nature, 2023,
pp. 231–64, doi:10.1007/s13235-022-00425-3.
short: T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023)
231–264.
date_created: 2022-02-20T23:01:32Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-10-04T09:24:30Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s13235-022-00425-3
ec_funded: 1
external_id:
isi:
- '000753777100001'
file:
- access_level: open_access
checksum: cd53b07e96f9030ddb348f305e5b58c7
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T08:54:17Z
date_updated: 2022-02-21T08:54:17Z
file_id: '10781'
file_name: 2022_DynamicGamesApplic_Graham.pdf
file_size: 1890512
relation: main_file
success: 1
file_date_updated: 2022-02-21T08:54:17Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 231-264
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Dynamic Games and Applications
publication_identifier:
eissn:
- 2153-0793
issn:
- 2153-0785
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Where do mistakes lead? A survey of games with incompetent players
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: 13
year: '2023'
...
---
_id: '10145'
abstract:
- lang: eng
text: We study direct integrals of quadratic and Dirichlet forms. We show that each
quasi-regular Dirichlet space over a probability space admits a unique representation
as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same
underlying topology. The same holds for each quasi-regular strongly local Dirichlet
space over a metrizable Luzin σ-finite Radon measure space, and admitting carré
du champ operator. In this case, the representation is only projectively unique.
acknowledgement: The author is grateful to Professors Sergio Albeverio and Andreas
Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the
present work, and for respectively pointing out the references [1, 13], and [3,
20]. Finally, he is especially grateful to an anonymous Reviewer for their very
careful reading and their suggestions which improved the readability of the paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
citation:
ama: Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals
and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y
apa: Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct
integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y
chicago: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct
Integrals and Applications.” Potential Analysis. Springer Nature, 2023.
https://doi.org/10.1007/s11118-021-09951-y.
ieee: L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals
and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615,
2023.
ista: Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct
integrals and applications. Potential Analysis. 58, 573–615.
mla: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct
Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature,
2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.
short: L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.
date_created: 2021-10-17T22:01:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-10-04T09:19:12Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s11118-021-09951-y
ec_funded: 1
external_id:
arxiv:
- '2003.01366'
isi:
- '000704213400001'
file:
- access_level: open_access
checksum: 625526482be300ca7281c91c30d41725
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:18:59Z
date_updated: 2023-10-04T09:18:59Z
file_id: '14387'
file_name: 2023_PotentialAnalysis_DelloSchiavo.pdf
file_size: 806391
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:18:59Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 573-615
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Potential Analysis
publication_identifier:
eissn:
- 1572-929X
issn:
- 0926-2601
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ergodic decomposition of Dirichlet forms via direct integrals and applications
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: 58
year: '2023'
...
---
_id: '12669'
abstract:
- lang: eng
text: The study of RNAs has become one of the most influential research fields in
contemporary biology and biomedicine. In the last few years, new sequencing technologies
have produced an explosion of new and exciting discoveries in the field but have
also given rise to many open questions. Defining these questions, together with
old, long-standing gaps in our knowledge, is the spirit of this article. The breadth
of topics within RNA biology research is vast, and every aspect of the biology
of these molecules contains countless exciting open questions. Here, we asked
12 groups to discuss their most compelling question among some plant RNA biology
topics. The following vignettes cover RNA alternative splicing; RNA dynamics;
RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding
RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis
and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each
section, we will present the current state-of-the-art in plant RNA biology research
before asking the questions that will surely motivate future discoveries in the
field. We hope this article will spark a debate about the future perspective on
RNA biology and provoke novel reflections in the reader.
article_number: koac346
article_processing_charge: No
article_type: original
author:
- first_name: Pablo A
full_name: Manavella, Pablo A
last_name: Manavella
- first_name: Micaela A
full_name: Godoy Herz, Micaela A
last_name: Godoy Herz
- first_name: Alberto R
full_name: Kornblihtt, Alberto R
last_name: Kornblihtt
- first_name: Reed
full_name: Sorenson, Reed
last_name: Sorenson
- first_name: Leslie E
full_name: Sieburth, Leslie E
last_name: Sieburth
- first_name: Kentaro
full_name: Nakaminami, Kentaro
last_name: Nakaminami
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Yiliang
full_name: Ding, Yiliang
last_name: Ding
- first_name: Qianwen
full_name: Sun, Qianwen
last_name: Sun
- first_name: Hunseung
full_name: Kang, Hunseung
last_name: Kang
- first_name: Federico D
full_name: Ariel, Federico D
last_name: Ariel
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Axel J
full_name: Giudicatti, Axel J
last_name: Giudicatti
- first_name: Qiang
full_name: Cai, Qiang
last_name: Cai
- first_name: Hailing
full_name: Jin, Hailing
last_name: Jin
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yijun
full_name: Qi, Yijun
last_name: Qi
- first_name: Craig S
full_name: Pikaard, Craig S
last_name: Pikaard
citation:
ama: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346'
apa: 'Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth,
L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. Oxford University
Press. https://doi.org/10.1093/plcell/koac346'
chicago: 'Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson,
Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription:
Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford
University Press, 2023. https://doi.org/10.1093/plcell/koac346.'
ieee: 'P. A. Manavella et al., “Beyond transcription: compelling open questions
in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University
Press, 2023.'
ista: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami
K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin
H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions
in plant RNA biology. The Plant Cell. 35(6), koac346.'
mla: 'Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions
in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford
University Press, 2023, doi:10.1093/plcell/koac346.'
short: P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth,
K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J.
Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).
date_created: 2023-02-23T09:14:59Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-10-04T09:48:43Z
day: '01'
department:
- _id: XiFe
doi: 10.1093/plcell/koac346
extern: '1'
external_id:
pmid:
- '36477566'
intvolume: ' 35'
issue: '6'
keyword:
- Cell Biology
- Plant Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/plcell/koac346
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond transcription: compelling open questions in plant RNA biology'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '11706'
abstract:
- lang: eng
text: 'We say that (Formula presented.) if, in every edge coloring (Formula presented.),
we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy
of (Formula presented.). The well-known states that the threshold for the property
(Formula presented.) is equal to (Formula presented.), where (Formula presented.)
is given by (Formula presented.) for any pair of graphs (Formula presented.) and
(Formula presented.) with (Formula presented.). In this article, we show the 0-statement
of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. '
acknowledgement: "This work was started at the thematic program GRAPHS@IMPA (January–March
2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and
for providing a pleasant research environment. We thank Rob Morris for helpful discussions,
and the anonymous referees for their careful reading and many helpful suggestions.
Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported
by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's
Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1,
project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Anita
full_name: Liebenau, Anita
last_name: Liebenau
- first_name: Letícia
full_name: Mattos, Letícia
last_name: Mattos
- first_name: Walner
full_name: Mendonca Dos Santos, Walner
id: 12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd
last_name: Mendonca Dos Santos
- first_name: Jozef
full_name: Skokan, Jozef
last_name: Skokan
citation:
ama: Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties
of random graphs involving cliques and cycles. Random Structures and Algorithms.
2023;62(4):1035-1055. doi:10.1002/rsa.21106
apa: Liebenau, A., Mattos, L., Mendonca dos Santos, W., & Skokan, J. (2023).
Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random
Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.21106
chicago: Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef
Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.”
Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106.
ieee: A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric
Ramsey properties of random graphs involving cliques and cycles,” Random Structures
and Algorithms, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.
ista: Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey
properties of random graphs involving cliques and cycles. Random Structures and
Algorithms. 62(4), 1035–1055.
mla: Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving
Cliques and Cycles.” Random Structures and Algorithms, vol. 62, no. 4,
Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106.
short: A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures
and Algorithms 62 (2023) 1035–1055.
date_created: 2022-07-31T22:01:49Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-10-04T09:38:45Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1002/rsa.21106
external_id:
isi:
- '000828530400001'
file:
- access_level: open_access
checksum: 3a5969d0c512aef01c30f3dc81c6d59b
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:37:26Z
date_updated: 2023-10-04T09:37:26Z
file_id: '14389'
file_name: 2023_RandomStructureAlgorithms_Liebenau.pdf
file_size: 1362334
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:37:26Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1035-1055
publication: Random Structures and Algorithms
publication_identifier:
eissn:
- 1098-2418
issn:
- 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymmetric Ramsey properties of random graphs involving cliques and cycles
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2023'
...
---
_id: '12707'
abstract:
- lang: eng
text: We establish precise right-tail small deviation estimates for the largest
eigenvalue of real symmetric and complex Hermitian matrices whose entries are
independent random variables with uniformly bounded moments. The proof relies
on a Green function comparison along a continuous interpolating matrix flow for
a long time. Less precise estimates are also obtained in the left tail.
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
orcid: 0000-0003-1559-1205
citation:
ama: Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner
matrices. Bernoulli. 2023;29(2):1063-1079. doi:10.3150/22-BEJ1490
apa: Erdös, L., & Xu, Y. (2023). Small deviation estimates for the largest eigenvalue
of Wigner matrices. Bernoulli. Bernoulli Society for Mathematical Statistics
and Probability. https://doi.org/10.3150/22-BEJ1490
chicago: Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest
Eigenvalue of Wigner Matrices.” Bernoulli. Bernoulli Society for Mathematical
Statistics and Probability, 2023. https://doi.org/10.3150/22-BEJ1490.
ieee: L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue
of Wigner matrices,” Bernoulli, vol. 29, no. 2. Bernoulli Society for Mathematical
Statistics and Probability, pp. 1063–1079, 2023.
ista: Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue
of Wigner matrices. Bernoulli. 29(2), 1063–1079.
mla: Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest
Eigenvalue of Wigner Matrices.” Bernoulli, vol. 29, no. 2, Bernoulli Society
for Mathematical Statistics and Probability, 2023, pp. 1063–79, doi:10.3150/22-BEJ1490.
short: L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079.
date_created: 2023-03-05T23:01:05Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T10:21:07Z
day: '01'
department:
- _id: LaEr
doi: 10.3150/22-BEJ1490
ec_funded: 1
external_id:
arxiv:
- '2112.12093 '
isi:
- '000947270100008'
intvolume: ' 29'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2112.12093
month: '05'
oa: 1
oa_version: Preprint
page: 1063-1079
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Bernoulli
publication_identifier:
issn:
- 1350-7265
publication_status: published
publisher: Bernoulli Society for Mathematical Statistics and Probability
quality_controlled: '1'
scopus_import: '1'
status: public
title: Small deviation estimates for the largest eigenvalue of Wigner matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2023'
...
---
_id: '12837'
abstract:
- lang: eng
text: As developing tissues grow in size and undergo morphogenetic changes, their
material properties may be altered. Such changes result from tension dynamics
at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms
controlling the physical state of growing tissues are unclear. We found that at
early developmental stages, the epithelium in the developing mouse spinal cord
maintains both high junctional tension and high fluidity. This is achieved via
a mechanism in which interkinetic nuclear movements generate cell area dynamics
that drive extensive cell rearrangements. Over time, the cell proliferation rate
declines, effectively solidifying the tissue. Thus, unlike well-studied jamming
transitions, the solidification uncovered here resembles a glass transition that
depends on the dynamical stresses generated by proliferation and differentiation.
Our finding that the fluidity of developing epithelia is linked to interkinetic
nuclear movements and the dynamics of growth is likely to be relevant to multiple
developing tissues.
acknowledgement: 'We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J.
Briscoe and K. Page for comments on the manuscript. This work was supported by IST
Austria; the European Research Council under Horizon 2020 research and innovation
programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science
Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.);
Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish
National Agency for Academic Exchange (M.Z.).'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Amrita
full_name: Singh, Amrita
id: 76250f9f-3a21-11eb-9a80-a6180a0d7958
last_name: Singh
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics
control fluidity of the developing mouse neuroepithelium. Nature Physics.
2023;19:1050-1058. doi:10.1038/s41567-023-01977-w
apa: Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A.
(2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w
chicago: Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and
Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.”
Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.
ieee: L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell
cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature
Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.
ista: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle
dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics.
19, 1050–1058.
mla: Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing
Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023,
pp. 1050–58, doi:10.1038/s41567-023-01977-w.
short: L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics
19 (2023) 1050–1058.
date_created: 2023-04-16T22:01:09Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-10-04T11:14:05Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
- _id: AnKi
doi: 10.1038/s41567-023-01977-w
ec_funded: 1
external_id:
isi:
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oa_version: Published Version
page: 1050-1058
project:
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call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
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grant_number: F07802
name: Morphogen control of growth and pattern in the spinal cord
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13081'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cell cycle dynamics control fluidity of the developing mouse neuroepithelium
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: 19
year: '2023'
...
---
_id: '13081'
abstract:
- lang: eng
text: During development, tissues undergo changes in size and shape to form functional
organs. Distinct cellular processes such as cell division and cell rearrangements
underlie tissue morphogenesis. Yet how the distinct processes are controlled and
coordinated, and how they contribute to morphogenesis is poorly understood. In
our study, we addressed these questions using the developing mouse neural tube.
This epithelial organ transforms from a flat epithelial sheet to an epithelial
tube while increasing in size and undergoing morpho-gen-mediated patterning. The
extent and mechanism of neural progenitor rearrangement within the developing
mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution
lineage tracing analysis to quantify the extent of epithelial rear-rangement at
different stages of neural tube development. We quantitatively described the relationship
between apical cell size with cell cycle dependent interkinetic nuclear migra-tions
(IKNM) and performed high cellular resolution live imaging of the neuroepithelium
to study the dynamics of junctional remodeling. Furthermore, developed a vertex
model of the neuroepithelium to investigate the quantitative contribution of cell
proliferation, cell differentiation and mechanical properties to the epithelial
rearrangement dynamics and validated the model predictions through functional
experiments. Our analysis revealed that at early developmental stages, the apical
cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in
a regime of high junctional tension and contractility. After E9.5, there is a
sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium
transitions from a fluid-like to a solid-like state. We found that this transition
is regulated by the growth rate of the tissue, rather than by changes in cell-cell
adhesion and contractile forces. Overall, our study provides a quantitative description
of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements
and the emergent tissue material properties, and novel insights on how epithelial
cell dynamics influences tissue morphogenesis.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
citation:
ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023.
doi:10.15479/at:ista:13081
apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081
chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.
ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,”
Institute of Science and Technology Austria, 2023.
ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria.
mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.
short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute
of Science and Technology Austria, 2023.
date_created: 2023-05-23T19:10:42Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2023-10-04T11:14:04Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
doi: 10.15479/at:ista:13081
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date_created: 2023-05-25T06:32:12Z
date_updated: 2023-05-25T06:32:12Z
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file_size: 25615534
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date_created: 2023-05-25T06:32:16Z
date_updated: 2023-05-25T06:32:16Z
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file_name: TotalFinal_Thesis_LauraBocanegraArx.pdf
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file_date_updated: 2023-05-25T06:32:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9349'
relation: part_of_dissertation
status: public
- id: '12837'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Epithelial dynamics during mouse neural tube development
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12836'
abstract:
- lang: eng
text: Coherent control and manipulation of quantum degrees of freedom such as spins
forms the basis of emerging quantum technologies. In this context, the robust
valley degree of freedom and the associated valley pseudospin found in two-dimensional
transition metal dichalcogenides is a highly attractive platform. Valley polarization
and coherent superposition of valley states have been observed in these systems
even up to room temperature. Control of valley coherence is an important building
block for the implementation of valley qubit. Large magnetic fields or high-power
lasers have been used in the past to demonstrate the control (initialization and
rotation) of the valley coherent states. Here, the control of layer–valley coherence
via strong coupling of valley excitons in bilayer WS2 to microcavity photons is
demonstrated by exploiting the pseudomagnetic field arising in optical cavities
owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The
use of photonic structures to generate pseudomagnetic fields which can be used
to manipulate exciton-polaritons presents an attractive approach to control optical
responses without the need for large magnets or high-intensity optical pump powers.
acknowledgement: The authors acknowledge insightful discussions with Prof. Wang Yao
and graphics by Rezlind Bushati. M.K. and N.Y. acknowledge support from NSF grants
NSF DMR-1709996 and NSF OMA 1936276. S.G. was supported by the Army Research Office
Multidisciplinary University Research Initiative program (W911NF-17-1-0312) and
V.M.M. by the Army Research Office grant (W911NF-22-1-0091). K.M acknowledges the
SPARC program that supported his collaboration with the CUNY team. The authors acknowledge
the Nanofabrication facility at the CUNY Advanced Science Research Center where
the cavity devices were fabricated.
article_number: '2202631'
article_processing_charge: No
article_type: original
author:
- first_name: Mandeep
full_name: Khatoniar, Mandeep
last_name: Khatoniar
- first_name: Nicholas
full_name: Yama, Nicholas
last_name: Yama
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Sriram
full_name: Guddala, Sriram
last_name: Guddala
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
- first_name: Kausik
full_name: Majumdar, Kausik
last_name: Majumdar
- first_name: Vinod
full_name: Menon, Vinod
last_name: Menon
citation:
ama: Khatoniar M, Yama N, Ghazaryan A, et al. Optical manipulation of Layer–Valley
coherence via strong exciton–photon coupling in microcavities. Advanced Optical
Materials. 2023;11(13). doi:10.1002/adom.202202631
apa: Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., Majumdar,
K., & Menon, V. (2023). Optical manipulation of Layer–Valley coherence via
strong exciton–photon coupling in microcavities. Advanced Optical Materials.
Wiley. https://doi.org/10.1002/adom.202202631
chicago: Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan
Ghaemi, Kausik Majumdar, and Vinod Menon. “Optical Manipulation of Layer–Valley
Coherence via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical
Materials. Wiley, 2023. https://doi.org/10.1002/adom.202202631.
ieee: M. Khatoniar et al., “Optical manipulation of Layer–Valley coherence
via strong exciton–photon coupling in microcavities,” Advanced Optical Materials,
vol. 11, no. 13. Wiley, 2023.
ista: Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Majumdar K, Menon V.
2023. Optical manipulation of Layer–Valley coherence via strong exciton–photon
coupling in microcavities. Advanced Optical Materials. 11(13), 2202631.
mla: Khatoniar, Mandeep, et al. “Optical Manipulation of Layer–Valley Coherence
via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical Materials,
vol. 11, no. 13, 2202631, Wiley, 2023, doi:10.1002/adom.202202631.
short: M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, K. Majumdar,
V. Menon, Advanced Optical Materials 11 (2023).
date_created: 2023-04-16T22:01:09Z
date_published: 2023-07-04T00:00:00Z
date_updated: 2023-10-04T11:15:17Z
day: '04'
department:
- _id: MiLe
doi: 10.1002/adom.202202631
external_id:
arxiv:
- '2211.08755'
isi:
- '000963866700001'
intvolume: ' 11'
isi: 1
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.08755
month: '07'
oa: 1
oa_version: Preprint
publication: Advanced Optical Materials
publication_identifier:
eissn:
- 2195-1071
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling
in microcavities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '12959'
abstract:
- lang: eng
text: "This paper deals with the large-scale behaviour of dynamical optimal transport
on Zd\r\n-periodic graphs with general lower semicontinuous and convex energy
densities. Our main contribution is a homogenisation result that describes the
effective behaviour of the discrete problems in terms of a continuous optimal
transport problem. The effective energy density can be explicitly expressed in
terms of a cell formula, which is a finite-dimensional convex programming problem
that depends non-trivially on the local geometry of the discrete graph and the
discrete energy density. Our homogenisation result is derived from a Γ\r\n-convergence
result for action functionals on curves of measures, which we prove under very
mild growth conditions on the energy density. We investigate the cell formula
in several cases of interest, including finite-volume discretisations of the Wasserstein
distance, where non-trivial limiting behaviour occurs."
acknowledgement: J.M. gratefully acknowledges support by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No. 716117). J.M and L.P. also acknowledge support from the Austrian
Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support
by the German Research Foundation through the Hausdorff Center for Mathematics and
the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche
Forschungsgemeinschaft (DFG, German Research Foundation)—350398276. We thank the
anonymous reviewer for the careful reading and for useful suggestions. Open access
funding provided by Austrian Science Fund (FWF).
article_number: '143'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Gladbach, Peter
last_name: Gladbach
- first_name: Eva
full_name: Kopfer, Eva
last_name: Kopfer
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of dynamical optimal
transport on periodic graphs. Calculus of Variations and Partial Differential
Equations. 2023;62(5). doi:10.1007/s00526-023-02472-z
apa: Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2023). Homogenisation
of dynamical optimal transport on periodic graphs. Calculus of Variations and
Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-023-02472-z
chicago: Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation
of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations
and Partial Differential Equations. Springer Nature, 2023. https://doi.org/10.1007/s00526-023-02472-z.
ieee: P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of dynamical
optimal transport on periodic graphs,” Calculus of Variations and Partial Differential
Equations, vol. 62, no. 5. Springer Nature, 2023.
ista: Gladbach P, Kopfer E, Maas J, Portinale L. 2023. Homogenisation of dynamical
optimal transport on periodic graphs. Calculus of Variations and Partial Differential
Equations. 62(5), 143.
mla: Gladbach, Peter, et al. “Homogenisation of Dynamical Optimal Transport on Periodic
Graphs.” Calculus of Variations and Partial Differential Equations, vol.
62, no. 5, 143, Springer Nature, 2023, doi:10.1007/s00526-023-02472-z.
short: P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Calculus of Variations and
Partial Differential Equations 62 (2023).
date_created: 2023-05-14T22:01:00Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-10-04T11:34:49Z
day: '28'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-023-02472-z
ec_funded: 1
external_id:
arxiv:
- '2110.15321'
isi:
- '000980588900001'
file:
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checksum: 359bee38d94b7e0aa73925063cb8884d
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T11:34:10Z
date_updated: 2023-10-04T11:34:10Z
file_id: '14393'
file_name: 2023_CalculusEquations_Gladbach.pdf
file_size: 1240995
relation: main_file
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file_date_updated: 2023-10-04T11:34:10Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '5'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _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
- _id: 260788DE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
name: Dissipation and Dispersion in Nonlinear Partial Differential Equations
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Homogenisation of dynamical optimal transport on periodic graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2023'
...