---
APC_amount: 11700 EUR
OA_place: publisher
OA_type: hybrid
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.
corr_author: '1'
date_created: 2024-02-12T09:59:45Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
isi:
- '001158144600002'
pmid:
- '38316877'
file:
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content_type: application/pdf
creator: dernst
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file_id: '17307'
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file_size: 17485494
relation: main_file
success: 1
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has_accepted_license: '1'
intvolume: ' 31'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1114-1123
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
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/down-to-the-core-of-poxviruses/
record:
- id: '18766'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
APC_amount: 2933,65 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '14980'
abstract:
- lang: eng
text: Precision sensing and manipulation of milligram-scale mechanical oscillators
has attracted growing interest in the fields of table-top explorations of gravity
and tests of quantum mechanics at macroscopic scales. Torsional oscillators present
an opportunity in this regard due to their remarked isolation from environmental
noise. For torsional motion, an effective employment of optical cavities to enhance
optomechanical interactions—as already established for linear oscillators—so far
faced certain challenges. Here, we propose a concept for sensing and manipulating
torsional motion, where exclusively the torsional rotations of a pendulum are
mapped onto the path length of a single two-mirror optical cavity. The concept
inherently alleviates many limitations of previous approaches. A proof-of-principle
experiment is conducted with a rigidly controlled pendulum to explore the sensing
aspects of the concept and to identify practical limitations in a potential state-of-the
art setup. Based on this study, we anticipate development of precision torque
sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz,
while the motion of the pendulums are dominated by quantum radiation pressure
noise at sub-microwatts of incoming laser power. These developments will provide
horizons for experiments at the interface of quantum mechanics and gravity.
acknowledgement: "We thank Pere Rosselló for his contributions to the initial modeling
of the presented sensing technique. This work was supported by Institute of Science
and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907
(ERC CoG QuHAMP)."
article_number: '013141'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Sofya
full_name: Agafonova, Sofya
id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80
last_name: Agafonova
orcid: 0000-0003-0582-2946
- first_name: Umang
full_name: Mishra, Umang
id: 4328fa4c-f128-11eb-9611-c107b0fe4d51
last_name: Mishra
- first_name: Fritz R
full_name: Diorico, Fritz R
id: 2E054C4C-F248-11E8-B48F-1D18A9856A87
last_name: Diorico
orcid: 0000-0002-4947-8924
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing
and controlling torsional motion. Physical Review Research. 2024;6(1).
doi:10.1103/physrevresearch.6.013141
apa: Agafonova, S., Mishra, U., Diorico, F. R., & Hosten, O. (2024). Zigzag
optical cavity for sensing and controlling torsional motion. Physical Review
Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013141
chicago: Agafonova, Sofya, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag
Optical Cavity for Sensing and Controlling Torsional Motion.” Physical Review
Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013141.
ieee: S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity
for sensing and controlling torsional motion,” Physical Review Research,
vol. 6, no. 1. American Physical Society, 2024.
ista: Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for
sensing and controlling torsional motion. Physical Review Research. 6(1), 013141.
mla: Agafonova, Sofya, et al. “Zigzag Optical Cavity for Sensing and Controlling
Torsional Motion.” Physical Review Research, vol. 6, no. 1, 013141, American
Physical Society, 2024, doi:10.1103/physrevresearch.6.013141.
short: S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research
6 (2024).
corr_author: '1'
date_created: 2024-02-12T11:42:18Z
date_published: 2024-02-05T00:00:00Z
date_updated: 2025-05-08T09:34:07Z
day: '05'
ddc:
- '530'
department:
- _id: OnHo
doi: 10.1103/physrevresearch.6.013141
external_id:
arxiv:
- '2306.12804'
file:
- access_level: open_access
checksum: 3a39ebffb24c1cc1dd0b547a726dc52d
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creator: dernst
date_created: 2024-02-12T11:46:50Z
date_updated: 2024-02-12T11:46:50Z
file_id: '14981'
file_name: 2024_PhysicalRevResearch_Agafonova.pdf
file_size: 1437167
relation: main_file
success: 1
file_date_updated: 2024-02-12T11:46:50Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6
grant_number: '101087907'
name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational
quantum mechanics'
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zigzag optical cavity for sensing and controlling torsional motion
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: 6
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '14986'
abstract:
- lang: eng
text: We prove a version of the tamely ramified geometric Langlands correspondence
in positive characteristic for GLn(k). Let k be an algebraically closed field
of characteristic p>n. Let X be a smooth projective curve over k with marked points,
and fix a parabolic subgroup of GLn(k) at each marked point. We denote by Bunn,P
the moduli stack of (quasi-)parabolic vector bundles on X, and by Locn,P the moduli
stack of parabolic flat connections such that the residue is nilpotent with respect
to the parabolic reduction at each marked point. We construct an equivalence between
the bounded derived category Db(Qcoh(Loc0n,P)) of quasi-coherent sheaves on an
open substack Loc0n,P⊂Locn,P, and the bounded derived category Db(D0Bunn,P-mod)
of D0Bunn,P-modules, where D0Bunn,P is a localization of DBunn,P the sheaf of
crystalline differential operators on Bunn,P. Thus we extend the work of Bezrukavnikov-Braverman
to the tamely ramified case. We also prove a correspondence between flat connections
on X with regular singularities and meromorphic Higgs bundles on the Frobenius
twist X(1) of X with first order poles .
acknowledgement: "This work was supported by the NSF [DMS-1502125to S.S.]; and the
European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
grant agreement [101034413 to S.S.].\r\nI would like to thank my advisor Tom Nevins
for many helpful discussions on this subject and for his comments on this paper.
I would like to thank Christopher Dodd, Michael Groechenig, and Tamas Hausel for
helpful conversations. I would like to thank Tsao-Hsien Chen for useful comments
on an earlier version of this paper."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Shiyu
full_name: Shen, Shiyu
id: 544cccd3-9005-11ec-87bc-94aef1c5b814
last_name: Shen
orcid: 0000-0002-4444-8718
citation:
ama: Shen S. Tamely ramified geometric Langlands correspondence in positive characteristic.
International Mathematics Research Notices. 2024;2024(7):6176-6208. doi:10.1093/imrn/rnae005
apa: Shen, S. (2024). Tamely ramified geometric Langlands correspondence in positive
characteristic. International Mathematics Research Notices. Oxford University
Press. https://doi.org/10.1093/imrn/rnae005
chicago: Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive
Characteristic.” International Mathematics Research Notices. Oxford University
Press, 2024. https://doi.org/10.1093/imrn/rnae005.
ieee: S. Shen, “Tamely ramified geometric Langlands correspondence in positive characteristic,”
International Mathematics Research Notices, vol. 2024, no. 7. Oxford University
Press, pp. 6176–6208, 2024.
ista: Shen S. 2024. Tamely ramified geometric Langlands correspondence in positive
characteristic. International Mathematics Research Notices. 2024(7), 6176–6208.
mla: Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive
Characteristic.” International Mathematics Research Notices, vol. 2024,
no. 7, Oxford University Press, 2024, pp. 6176–208, doi:10.1093/imrn/rnae005.
short: S. Shen, International Mathematics Research Notices 2024 (2024) 6176–6208.
corr_author: '1'
date_created: 2024-02-14T12:16:17Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-09-09T08:30:06Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1093/imrn/rnae005
ec_funded: 1
external_id:
arxiv:
- '1810.12491'
isi:
- '001157898100001'
file:
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file_id: '17308'
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file_size: 1488981
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success: 1
file_date_updated: 2024-07-22T11:41:57Z
has_accepted_license: '1'
intvolume: ' 2024'
isi: 1
issue: '7'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 6176-6208
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: International Mathematics Research Notices
publication_identifier:
eissn:
- 1687-0247
issn:
- 1073-7928
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tamely ramified geometric Langlands correspondence in positive characteristic
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: 2024
year: '2024'
...
---
APC_amount: 5936,71 EUR
OA_place: publisher
OA_type: hybrid
_id: '15001'
abstract:
- lang: eng
text: "Self-replication of amyloid fibrils via secondary nucleation is an intriguing
physicochemical phenomenon in which existing fibrils catalyze the formation of
their own copies. The molecular events behind this fibril surface-mediated process
remain largely inaccessible to current structural and imaging techniques. Using
statistical mechanics, computer modeling, and chemical kinetics, we show that
the catalytic structure of the fibril surface can be inferred from the aggregation
behavior in the presence and absence of a fibril-binding inhibitor. We apply our
approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence
of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils
occurs on small catalytic sites on the fibril surface, which are far apart from
each other, and each of which can be covered by a single Brichos inhibitor."
acknowledgement: We acknowledge support from the Erasmus programme and the University
College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.),
the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering
and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K.,
S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C.
and A.Š.).
article_number: e2220075121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Samo
full_name: Curk, Samo
id: 031eff0d-d481-11ee-8508-cd12a7a86e5b
last_name: Curk
orcid: 0000-0001-6160-9766
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs
on small and isolated fibril sites. Proceedings of the National Academy of
Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121
apa: Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C.
T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and
isolated fibril sites. Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121
chicago: Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas
C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42
Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2220075121.
ieee: S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small
and isolated fibril sites,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 121, no. 7. National Academy of Sciences,
2024.
ista: Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ,
Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated
fibril sites. Proceedings of the National Academy of Sciences of the United States
of America. 121(7), e2220075121.
mla: Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and
Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 7, e2220075121, National Academy
of Sciences, 2024, doi:10.1073/pnas.2220075121.
short: S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J.
Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United
States of America 121 (2024).
corr_author: '1'
date_created: 2024-02-18T23:01:00Z
date_published: 2024-02-13T00:00:00Z
date_updated: 2025-09-04T12:03:12Z
day: '13'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2220075121
ec_funded: 1
external_id:
isi:
- '001169063600007'
pmid:
- '38335256'
file:
- access_level: open_access
checksum: 5aeb65bcc0dd829b1f9ab307c5031d4b
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T08:20:00Z
date_updated: 2024-02-26T08:20:00Z
file_id: '15026'
file_name: 2024_PNAS_Curk.pdf
file_size: 7699487
relation: main_file
success: 1
file_date_updated: 2024-02-26T08:20:00Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
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scopus_import: '1'
status: public
title: Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
_id: '15002'
abstract:
- lang: eng
text: "The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n
dimensions, is a well-studied test bench for lattice gauge theories. Here, we
study the fractal properties of this model. We reveal the self-similarity of the
ground state, which allows us to develop a recurrent procedure for finding the
ground-state wave functions and predicting ground-state energies. We present the
results of recurrently calculating ground-state wave functions using the fractal
Ansatz and automized software package for fractal image processing. In certain
parameter regimes, just a few terms are enough for our recurrent procedure to
predict ground-state energies close to the exact ones for several hundreds of
sites. Our findings pave the way to understanding the complexity of calculating
many-body wave functions in terms of their fractal properties as well as finding
new links between condensed matter and high-energy lattice models."
acknowledgement: "We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions
and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase
structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful
comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No.
20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract
No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks
the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027.
M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868."
article_number: '050401'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Petrova, Elena
id: 0ac84990-897b-11ed-a09c-f5abb56a4ede
last_name: Petrova
- first_name: Egor S.
full_name: Tiunov, Egor S.
last_name: Tiunov
- first_name: Mari Carmen
full_name: Bañuls, Mari Carmen
last_name: Bañuls
- first_name: Aleksey K.
full_name: Fedorov, Aleksey K.
last_name: Fedorov
citation:
ama: Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger
model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401
apa: Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal
states of the Schwinger model. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.132.050401
chicago: Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov.
“Fractal States of the Schwinger Model.” Physical Review Letters. American
Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401.
ieee: E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states
of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American
Physical Society, 2024.
ista: Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger
model. Physical Review Letters. 132(5), 050401.
mla: Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical
Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024,
doi:10.1103/PhysRevLett.132.050401.
short: E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters
132 (2024).
date_created: 2024-02-18T23:01:00Z
date_published: 2024-01-30T00:00:00Z
date_updated: 2025-09-04T12:02:33Z
day: '30'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.132.050401
external_id:
arxiv:
- '2201.10220'
isi:
- '001179276700003'
pmid:
- '38364163'
intvolume: ' 132'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.10220
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fractal states of the Schwinger model
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 132
year: '2024'
...
---
_id: '15003'
abstract:
- lang: eng
text: Magnetic frustration allows to access novel and intriguing properties of magnetic
systems and has been explored mainly in planar triangular-like arrays of magnetic
ions. In this work, we describe the phosphide Ce6Ni6P17, where the Ce+3 ions accommodate
in a body-centered cubic lattice of Ce6 regular octahedra. From measurements of
magnetization, specific heat, and resistivity, we determine a rich phase diagram
as a function of temperature and magnetic field in which different magnetic phases
are found. Besides clear evidence of magnetic frustration is obtained from entropy
analysis. At zero field, a second-order antiferromagnetic transition occurs at
TN1≈1 K followed by a first-order transition at TN2≈0.45 K. With magnetic field
new magnetic phases appear, including a weakly first-order transition which ends
in a classical critical point and a third magnetic phase. We also study the exact
solution of the spin-1/2 Heisenberg model in an octahedron which allows us a qualitative
understanding of the phase diagram and compare with the experimental results.
acknowledgement: "The authors thank Bernardo Pentke for the SEM micrographs (Departamento
Fisicoquímica de Materiales CABCNEA). We are indebted to Julián Sereni for useful
discussions. D. G. F. acknowledges financial support provided by Agencia I+D+i,
Argentina, Grant No. PICT-2021-I-INVI00852 and Universidad Nacional de Cuyo (SIIP)
Grant No. 06/C018-T1. A. A. A. acknowledges financial support provided by PICT 2018-01546
and PICT 2020A-03661 of the\r\nAgencia I+D+i. "
article_number: '054405'
article_processing_charge: No
article_type: original
author:
- first_name: D. G.
full_name: Franco, D. G.
last_name: Franco
- first_name: R.
full_name: Avalos, R.
last_name: Avalos
- first_name: D.
full_name: Hafner, D.
last_name: Hafner
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Yu
full_name: Prots, Yu
last_name: Prots
- first_name: O.
full_name: Stockert, O.
last_name: Stockert
- first_name: A.
full_name: Hoser, A.
last_name: Hoser
- first_name: P. J.W.
full_name: Moll, P. J.W.
last_name: Moll
- first_name: M.
full_name: Brando, M.
last_name: Brando
- first_name: A. A.
full_name: Aligia, A. A.
last_name: Aligia
- first_name: C.
full_name: Geibel, C.
last_name: Geibel
citation:
ama: Franco DG, Avalos R, Hafner D, et al. Frustrated magnetism in octahedra-based
Ce6 Ni6 P17. Physical Review B. 2024;109(5). doi:10.1103/PhysRevB.109.054405
apa: Franco, D. G., Avalos, R., Hafner, D., Modic, K. A., Prots, Y., Stockert, O.,
… Geibel, C. (2024). Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical
Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.109.054405
chicago: Franco, D. G., R. Avalos, D. Hafner, Kimberly A Modic, Yu Prots, O. Stockert,
A. Hoser, et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” Physical
Review B. American Physical Society, 2024. https://doi.org/10.1103/PhysRevB.109.054405.
ieee: D. G. Franco et al., “Frustrated magnetism in octahedra-based Ce6 Ni6
P17,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.
ista: Franco DG, Avalos R, Hafner D, Modic KA, Prots Y, Stockert O, Hoser A, Moll
PJW, Brando M, Aligia AA, Geibel C. 2024. Frustrated magnetism in octahedra-based
Ce6 Ni6 P17. Physical Review B. 109(5), 054405.
mla: Franco, D. G., et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.”
Physical Review B, vol. 109, no. 5, 054405, American Physical Society,
2024, doi:10.1103/PhysRevB.109.054405.
short: D.G. Franco, R. Avalos, D. Hafner, K.A. Modic, Y. Prots, O. Stockert, A.
Hoser, P.J.W. Moll, M. Brando, A.A. Aligia, C. Geibel, Physical Review B 109 (2024).
date_created: 2024-02-18T23:01:01Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-09-04T12:05:01Z
day: '01'
department:
- _id: KiMo
doi: 10.1103/PhysRevB.109.054405
external_id:
isi:
- '001198571800008'
intvolume: ' 109'
isi: 1
issue: '5'
language:
- iso: eng
month: '02'
oa_version: None
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: Frustrated magnetism in octahedra-based Ce6 Ni6 P17
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 109
year: '2024'
...
---
_id: '15004'
abstract:
- lang: eng
text: The impulsive limit (the “sudden approximation”) has been widely employed
to describe the interaction between molecules and short, far-off-resonant laser
pulses. This approximation assumes that the timescale of the laser-molecule interaction
is significantly shorter than the internal rotational period of the molecule,
resulting in the rotational motion being instantaneously “frozen” during the interaction.
This simplified description of the laser-molecule interaction is incorporated
in various theoretical models predicting rotational dynamics of molecules driven
by short laser pulses. In this theoretical work, we develop an effective theory
for ultrashort laser pulses by examining the full time-evolution operator and
solving the time-dependent Schrödinger equation at the operator level. Our findings
reveal a critical angular momentum, lcrit, at which the impulsive limit breaks
down. In other words, the validity of the sudden approximation depends not only
on the pulse duration but also on its intensity, since the latter determines how
many angular momentum states are populated. We explore both ultrashort multicycle
(Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce
distinct effective potentials. We discuss the limitations of the impulsive limit
and propose a method that rescales the effective matrix elements, enabling an
improved and more accurate description of laser-molecule interactions.
acknowledgement: We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev,
and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the
European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).
article_number: '023101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: 'Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive
limit in molecular rotational dynamics. Physical Review A. 2024;109(2).
doi:10.1103/PhysRevA.109.023101'
apa: 'Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating
the impulsive limit in molecular rotational dynamics. Physical Review A.
American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101'
chicago: 'Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks:
Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical
Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.'
ieee: 'V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating
the impulsive limit in molecular rotational dynamics,” Physical Review A,
vol. 109, no. 2. American Physical Society, 2024.'
ista: 'Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating
the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2),
023101.'
mla: 'Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating
the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A,
vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.'
short: V. Karle, M. Lemeshko, Physical Review A 109 (2024).
corr_author: '1'
date_created: 2024-02-18T23:01:01Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2026-04-07T11:48:53Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.109.023101
ec_funded: 1
external_id:
arxiv:
- '2307.07256'
isi:
- '001158043800006'
intvolume: ' 109'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.07256
month: '02'
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'
related_material:
record:
- id: '19393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular
rotational dynamics'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 109
year: '2024'
...
---
_id: '15006'
abstract:
- lang: eng
text: Graphical games are a useful framework for modeling the interactions of (selfish)
agents who are connected via an underlying topology and whose behaviors influence
each other. They have wide applications ranging from computer science to economics
and biology. Yet, even though an agent’s payoff only depends on the actions of
their direct neighbors in graphical games, computing the Nash equilibria and making
statements about the convergence time of "natural" local dynamics in particular
can be highly challenging. In this work, we present a novel approach for classifying
complexity of Nash equilibria in graphical games by establishing a connection
to local graph algorithms, a subfield of distributed computing. In particular,
we make the observation that the equilibria of graphical games are equivalent
to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable
with constant-round local algorithms. This connection allows us to derive novel
lower bounds on the convergence time to equilibrium of best-response dynamics
in graphical games. Since we establish that distributed convergence can sometimes
be provably slow, we also introduce and give bounds on an intuitive notion of
"time-constrained" inefficiency of best responses. We exemplify how our results
can be used in the implementation of mechanisms that ensure convergence of best
responses to a Nash equilibrium. Our results thus also give insight into the convergence
of strategy-proof algorithms for graphical games, which is still not well understood.
acknowledgement: This work was partially funded by the Academy of Finland, grant 314888,
the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science
Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis
and Application Research Center (SAARC) under National Research Foundation of Korea
grant NRF-2019R1A5A1028324.
alternative_title:
- LIPIcs
article_number: '11'
article_processing_charge: No
arxiv: 1
author:
- first_name: Juho
full_name: Hirvonen, Juho
last_name: Hirvonen
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical
games: A locality-sensitive approach. In: 27th International Conference on
Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.11'
apa: 'Hirvonen, J., Schmid, L., Chatterjee, K., & Schmid, S. (2024). On the
convergence time in graphical games: A locality-sensitive approach. In 27th
International Conference on Principles of Distributed Systems (Vol. 286).
Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11'
chicago: 'Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid.
“On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” In
27th International Conference on Principles of Distributed Systems, Vol.
286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.11.'
ieee: 'J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence
time in graphical games: A locality-sensitive approach,” in 27th International
Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol.
286.'
ista: 'Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time
in graphical games: A locality-sensitive approach. 27th International Conference
on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed
Systems, LIPIcs, vol. 286, 11.'
mla: 'Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive
Approach.” 27th International Conference on Principles of Distributed Systems,
vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.11.'
short: J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International
Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024.
conference:
end_date: 2023-12-08
location: Tokyo, Japan
name: 'OPODIS: Conference on Principles of Distributed Systems'
start_date: 2023-12-06
corr_author: '1'
date_created: 2024-02-18T23:01:01Z
date_published: 2024-01-18T00:00:00Z
date_updated: 2025-12-02T13:38:16Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.OPODIS.2023.11
ec_funded: 1
external_id:
arxiv:
- '2102.13457'
isi:
- '001585185800011'
file:
- access_level: open_access
checksum: 4fc7eea6e4ba140b904781fc7df868ec
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T09:04:58Z
date_updated: 2024-02-26T09:04:58Z
file_id: '15028'
file_name: 2024_LIPICs_Hirvonen.pdf
file_size: 867363
relation: main_file
success: 1
file_date_updated: 2024-02-26T09:04:58Z
has_accepted_license: '1'
intvolume: ' 286'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 27th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959773089'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'On the convergence time in graphical games: A locality-sensitive approach'
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: 286
year: '2024'
...
---
_id: '15007'
abstract:
- lang: eng
text: Traditional blockchains grant the miner of a block full control not only over
which transactions but also their order. This constitutes a major flaw discovered
with the introduction of decentralized finance and allows miners to perform MEV
attacks. In this paper, we address the issue of sandwich attacks by providing
a construction that takes as input a blockchain protocol and outputs a new blockchain
protocol with the same security but in which sandwich attacks are not profitable.
Furthermore, our protocol is fully decentralized with no trusted third parties
or heavy cryptography primitives and carries a linear increase in latency and
minimum computation overhead.
acknowledgement: "We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful
discussions. This work has been funded by the Swiss National Science Foundation
(SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n"
alternative_title:
- LIPIcs
article_number: '12'
article_processing_charge: No
arxiv: 1
author:
- first_name: Orestis
full_name: Alpos, Orestis
last_name: Alpos
- first_name: Ignacio
full_name: Amores-Sesar, Ignacio
last_name: Amores-Sesar
- first_name: Christian
full_name: Cachin, Christian
last_name: Cachin
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: 'Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and
lightweight elimination of transaction reordering attacks. In: 27th International
Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12'
apa: 'Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches:
Modular and lightweight elimination of transaction reordering attacks. In 27th
International Conference on Principles of Distributed Systems (Vol. 286).
Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12'
chicago: 'Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X
Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering
Attacks.” In 27th International Conference on Principles of Distributed Systems,
Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12.'
ieee: 'O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches:
Modular and lightweight elimination of transaction reordering attacks,” in 27th
International Conference on Principles of Distributed Systems, Tokyo, Japan,
2024, vol. 286.'
ista: 'Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular
and lightweight elimination of transaction reordering attacks. 27th International
Conference on Principles of Distributed Systems. OPODIS: Conference on Principles
of Distributed Systems, LIPIcs, vol. 286, 12.'
mla: 'Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination
of Transaction Reordering Attacks.” 27th International Conference on Principles
of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12.'
short: O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference
on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024.
conference:
end_date: 2023-12-08
location: Tokyo, Japan
name: 'OPODIS: Conference on Principles of Distributed Systems'
start_date: 2023-12-06
corr_author: '1'
date_created: 2024-02-18T23:01:02Z
date_published: 2024-01-18T00:00:00Z
date_updated: 2025-12-02T13:38:53Z
day: '18'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPIcs.OPODIS.2023.12
external_id:
arxiv:
- '2307.02954'
isi:
- '001585185800012'
file:
- access_level: open_access
checksum: 2993e810a45e8c8056106834b07aea92
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T10:16:57Z
date_updated: 2024-02-26T10:16:57Z
file_id: '15031'
file_name: 2024_LIPICs_Alpos.pdf
file_size: 1505994
relation: main_file
success: 1
file_date_updated: 2024-02-26T10:16:57Z
has_accepted_license: '1'
intvolume: ' 286'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: 27th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959773089'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Eating sandwiches: Modular and lightweight elimination of transaction reordering
attacks'
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: 286
year: '2024'
...
---
_id: '15008'
abstract:
- lang: eng
text: "Oblivious routing is a well-studied paradigm that uses static precomputed
routing tables for selecting routing paths within a network. Existing oblivious
routing schemes with polylogarithmic competitive ratio for general networks are
tree-based, in the sense that routing is performed according to a convex combination
of trees. However, this restriction to trees leads to a construction that has
time quadratic in the size of the network and does not parallelize well. \r\nIn
this paper we study oblivious routing schemes based on electrical routing. In
particular, we show that general networks with n vertices and m edges admit a
routing scheme that has competitive ratio O(log² n) and consists of a convex combination
of only O(√m) electrical routings. This immediately leads to an improved construction
algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with
Õ(√m) depth."
acknowledgement: "Monika Henzinger and A. R. Sricharan: This project has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the
Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P
33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald
Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets),
2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and
Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398
and a Sloan Research Fellowship."
alternative_title:
- LIPIcs
article_number: '55'
article_processing_charge: No
arxiv: 1
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
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: Sushant
full_name: Sachdeva, Sushant
last_name: Sachdeva
- first_name: A. R.
full_name: Sricharan, A. R.
last_name: Sricharan
citation:
ama: 'Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. Electrical flows
for polylogarithmic competitive oblivious routing. In: 15th Innovations in
Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55'
apa: 'Goranci, G., Henzinger, M., Räcke, H., Sachdeva, S., & Sricharan, A. R.
(2024). Electrical flows for polylogarithmic competitive oblivious routing. In
15th Innovations in Theoretical Computer Science Conference (Vol. 287).
Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.ITCS.2024.55'
chicago: Goranci, Gramoz, Monika Henzinger, Harald Räcke, Sushant Sachdeva, and
A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.”
In 15th Innovations in Theoretical Computer Science Conference, Vol. 287.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.
ieee: G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical
flows for polylogarithmic competitive oblivious routing,” in 15th Innovations
in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024,
vol. 287.
ista: 'Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical
flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical
Computer Science Conference. ITCS: Innovations in Theoretical Computer Science,
LIPIcs, vol. 287, 55.'
mla: Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious
Routing.” 15th Innovations in Theoretical Computer Science Conference,
vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55.
short: G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th
Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024.
conference:
end_date: 2024-02-02
location: Berkeley, CA, United States
name: 'ITCS: Innovations in Theoretical Computer Science'
start_date: 2024-01-30
corr_author: '1'
date_created: 2024-02-18T23:01:02Z
date_published: 2024-01-24T00:00:00Z
date_updated: 2025-09-04T12:06:25Z
day: '24'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ITCS.2024.55
ec_funded: 1
external_id:
arxiv:
- '2303.02491'
isi:
- '001300389400055'
file:
- access_level: open_access
checksum: b89716aae6a5599f187897e39de1e53a
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T10:10:48Z
date_updated: 2024-02-26T10:10:48Z
file_id: '15030'
file_name: 2024_LIPICs_Goranci.pdf
file_size: 1054754
relation: main_file
success: 1
file_date_updated: 2024-02-26T10:10:48Z
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
language:
- iso: eng
month: '01'
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: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _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: 15th Innovations in Theoretical Computer Science Conference
publication_identifier:
isbn:
- '9783959773096'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electrical flows for polylogarithmic competitive oblivious routing
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...
---
_id: '15011'
abstract:
- lang: eng
text: Pruning large language models (LLMs) from the BERT family has emerged as a
standard compression benchmark, and several pruning methods have been proposed
for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question
the validity of all existing methods, exhibiting a more complex setup where many
known pruning methods appear to fail. We revisit the question of accurate BERT-pruning
during fine-tuning on downstream datasets, and propose a set of general guidelines
for successful pruning, even on the challenging SMC benchmark. First, we perform
a cost-vs-benefits analysis of pruning model components, such as the embeddings
and the classification head; second, we provide a simple-yet-general way of scaling
training, sparsification and learning rate schedules relative to the desired target
sparsity; finally, we investigate the importance of proper parametrization for
Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art
results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark,
showing that even classic gradual magnitude pruning (GMP) can yield competitive
results, with the right approach.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering
accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning
Research. Vol 234. ML Research Press; 2024:542-553.'
apa: 'Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language
model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings
of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML
Research Press.'
chicago: 'Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune
Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.”
In Proceedings of Machine Learning Research, 234:542–53. ML Research Press,
2024.'
ieee: 'E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model:
Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of
Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.'
ista: 'Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model:
Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine
Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234,
542–553.'
mla: 'Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy
on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research,
vol. 234, ML Research Press, 2024, pp. 542–53.'
short: E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning
Research, ML Research Press, 2024, pp. 542–553.
conference:
end_date: 2024-01-06
location: Hongkong, China
name: 'CPAL: Conference on Parsimony and Learning'
start_date: 2024-01-03
corr_author: '1'
date_created: 2024-02-18T23:01:03Z
date_published: 2024-01-08T00:00:00Z
date_updated: 2024-10-09T21:08:16Z
day: '08'
department:
- _id: DaAl
external_id:
arxiv:
- '2312.13547'
intvolume: ' 234'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.mlr.press/v234/kurtic24a
month: '01'
oa: 1
oa_version: Preprint
page: 542-553
publication: Proceedings of Machine Learning Research
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'How to prune your language model: Recovering accuracy on the "Sparsity May
Cry" benchmark'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 234
year: '2024'
...
---
_id: '15012'
abstract:
- lang: eng
text: We solve a problem of Dujmović and Wood (2007) by showing that a complete
convex geometric graph on n vertices cannot be decomposed into fewer than n-1
star-forests, each consisting of noncrossing edges. This bound is clearly tight.
We also discuss similar questions for abstract graphs.
acknowledgement: János Pach’s Research partially supported by European Research Council
(ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH),
grant K-131529. Work by Morteza Saghafian is partially supported by the European
Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian
Science Fund (FWF), grant No. Z 342-N31.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
- first_name: Patrick
full_name: Schnider, Patrick
last_name: Schnider
citation:
ama: 'Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests.
In: 31st International Symposium on Graph Drawing and Network Visualization.
Vol 14465. Springer Nature; 2024:339-346. doi:10.1007/978-3-031-49272-3_23'
apa: 'Pach, J., Saghafian, M., & Schnider, P. (2024). Decomposition of geometric
graphs into star-forests. In 31st International Symposium on Graph Drawing
and Network Visualization (Vol. 14465, pp. 339–346). Isola delle Femmine,
Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49272-3_23'
chicago: Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric
Graphs into Star-Forests.” In 31st International Symposium on Graph Drawing
and Network Visualization, 14465:339–46. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49272-3_23.
ieee: J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs
into star-forests,” in 31st International Symposium on Graph Drawing and Network
Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp.
339–346.
ista: 'Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs
into star-forests. 31st International Symposium on Graph Drawing and Network Visualization.
GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.'
mla: Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.”
31st International Symposium on Graph Drawing and Network Visualization,
vol. 14465, Springer Nature, 2024, pp. 339–46, doi:10.1007/978-3-031-49272-3_23.
short: J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on
Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.
conference:
end_date: 2023-09-22
location: Isola delle Femmine, Palermo, Italy
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2023-09-20
date_created: 2024-02-18T23:01:03Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2026-04-16T09:12:37Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-031-49272-3_23
ec_funded: 1
external_id:
arxiv:
- '2306.13201'
isi:
- '001207939600023'
intvolume: ' 14465'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.13201
month: '01'
oa: 1
oa_version: Preprint
page: 339-346
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: Mathematics, Computer Science
publication: 31st International Symposium on Graph Drawing and Network Visualization
publication_identifier:
eisbn:
- '9783031492723'
eissn:
- 1611-3349
isbn:
- '9783031492716'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '21253'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Decomposition of geometric graphs into star-forests
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 14465
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15018'
abstract:
- lang: eng
text: The epitaxial growth of a strained Ge layer, which is a promising candidate
for the channel material of a hole spin qubit, has been demonstrated on 300 mm
Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB)
layers. The assessment of the layer and the interface qualities for a buried strained
Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping
confirmed that the reduction of the growth temperature enables the 2-dimensional
growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless,
dislocations at the top and/or bottom interface of the Ge layer were observed
by means of electron channeling contrast imaging, suggesting the importance of
the careful dislocation assessment. The interface abruptness does not depend on
the selection of the precursor gases, but it is strongly influenced by the growth
temperature which affects the coverage of the surface H-passivation. The mobility
of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010
/cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the
heterostructure thanks to the high Si0.3Ge0.7 SRB quality.
acknowledgement: The Ge project received funding from the European Union's Horizon
Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged
for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation
Program on Quantum Computing.
article_number: '108231'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yosuke
full_name: Shimura, Yosuke
last_name: Shimura
- first_name: Clement
full_name: Godfrin, Clement
last_name: Godfrin
- first_name: Andriy
full_name: Hikavyy, Andriy
last_name: Hikavyy
- first_name: Roy
full_name: Li, Roy
last_name: Li
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Paola
full_name: Favia, Paola
last_name: Favia
- first_name: Han
full_name: Han, Han
last_name: Han
- first_name: Danny
full_name: Wan, Danny
last_name: Wan
- first_name: Kristiaan
full_name: de Greve, Kristiaan
last_name: de Greve
- first_name: Roger
full_name: Loo, Roger
last_name: Loo
citation:
ama: Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge
layers for quantum computing applications. Materials Science in Semiconductor
Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231
apa: Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros,
G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing
applications. Materials Science in Semiconductor Processing. Elsevier.
https://doi.org/10.1016/j.mssp.2024.108231
chicago: Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera
Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial
Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor
Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.
ieee: Y. Shimura et al., “Compressively strained epitaxial Ge layers for
quantum computing applications,” Materials Science in Semiconductor Processing,
vol. 174, no. 5. Elsevier, 2024.
ista: Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia
P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge
layers for quantum computing applications. Materials Science in Semiconductor
Processing. 174(5), 108231.
mla: Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum
Computing Applications.” Materials Science in Semiconductor Processing,
vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.
short: Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros,
P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor
Processing 174 (2024).
date_created: 2024-02-22T14:10:40Z
date_published: 2024-05-20T00:00:00Z
date_updated: 2025-04-14T08:01:27Z
day: '20'
ddc:
- '530'
department:
- _id: GeKa
- _id: NanoFab
doi: 10.1016/j.mssp.2024.108231
external_id:
isi:
- '001188520000001'
file:
- access_level: open_access
checksum: 62e8e9ae960387a3dca32ec7f5e413ab
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:56:08Z
date_updated: 2024-07-22T11:56:08Z
file_id: '17312'
file_name: 2024_MaterialsScience_Shimura.pdf
file_size: 4220165
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:56:08Z
has_accepted_license: '1'
intvolume: ' 174'
isi: 1
issue: '5'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
publication: Materials Science in Semiconductor Processing
publication_identifier:
issn:
- 1369-8001
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Compressively strained epitaxial Ge layers for quantum computing 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: 174
year: '2024'
...
---
OA_place: publisher
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2026-04-07T12:59:25Z
day: '23'
ddc:
- '576'
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
success: 1
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checksum: eda9b9430da2610fee7ce1c1419a479a
content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7606'
relation: part_of_dissertation
status: public
- id: '12081'
relation: part_of_dissertation
status: public
- id: '7553'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
_id: '15024'
abstract:
- lang: eng
text: Electrostatic correlations between ions dissolved in water are known to impact
their transport properties in numerous ways, from conductivity to ion selectivity.
The effects of these correlations on the solvent itself remain, however, much
less clear. In particular, the addition of salt has been consistently reported
to affect the solution’s viscosity, but most modeling attempts fail to reproduce
experimental data even at moderate salt concentrations. Here, we use an approach
based on stochastic density functional theory, which accurately captures charge
fluctuations and correlations. We derive a simple analytical expression for the
viscosity correction in concentrated electrolytes, by directly linking it to the
liquid’s structure factor. Our prediction compares quantitatively to experimental
data at all temperatures and all salt concentrations up to the saturation limit.
This universal link between the microscopic structure and viscosity allows us
to shed light on the nanoscale dynamics of water and ions under highly concentrated
and correlated conditions.
acknowledgement: The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu
Lizée for fruitful discussions. This project received funding from the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
article_number: '064503'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
citation:
ama: Robin P. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215
apa: Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215
chicago: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.
ieee: P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,”
Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.
ista: Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 160(6), 064503.
mla: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024,
doi:10.1063/5.0188215.
short: P. Robin, Journal of Chemical Physics 160 (2024).
corr_author: '1'
date_created: 2024-02-25T23:00:55Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2025-09-04T12:07:33Z
day: '14'
ddc:
- '540'
department:
- _id: EdHa
doi: 10.1063/5.0188215
ec_funded: 1
external_id:
arxiv:
- '2311.11784'
isi:
- '001161104900003'
pmid:
- '38349632'
file:
- access_level: open_access
checksum: 0a5e0ae70849bce674466fc054390ec0
content_type: application/pdf
creator: dernst
date_created: 2024-02-27T08:12:52Z
date_updated: 2024-02-27T08:12:52Z
file_id: '15034'
file_name: 2024_JourChemicalPhysics_Robin.pdf
file_size: 5452738
relation: main_file
success: 1
file_date_updated: 2024-02-27T08:12:52Z
has_accepted_license: '1'
intvolume: ' 160'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 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: Correlation-induced viscous dissipation in concentrated electrolytes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 160
year: '2024'
...
---
_id: '15025'
abstract:
- lang: eng
text: We consider quadratic forms of deterministic matrices A evaluated at the random
eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the
columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as
long as the deterministic matrix has rank much smaller than √N, the distributions
of the extrema of these quadratic forms are asymptotically the same as if the
eigenvectors were independent Gaussians. This reduces the problem to Gaussian
computations, which we carry out in several cases to illustrate our result, finding
Gumbel or Weibull limiting distributions depending on the signature of A. Our
result also naturally applies to the eigenvectors of any invariant ensemble.
acknowledgement: The first author was supported by the ERC Advanced Grant “RMTBeyond”
No. 101020331. The second author was supported by Fulbright Austria and the Austrian
Marshall Plan Foundation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Benjamin
full_name: McKenna, Benjamin
id: b0cc634c-d549-11ee-96c8-87338c7ad808
last_name: McKenna
orcid: 0000-0003-2625-495X
citation:
ama: Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors.
Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000
apa: Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms
of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/23-AAP2000
chicago: Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic
Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute
of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000.
ieee: L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE
eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute
of Mathematical Statistics, pp. 1623–1662, 2024.
ista: Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE
eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.
mla: Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms
of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B,
Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000.
short: L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.
corr_author: '1'
date_created: 2024-02-25T23:00:56Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-09-04T12:08:11Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/23-AAP2000
ec_funded: 1
external_id:
arxiv:
- '2208.12206'
isi:
- '001163006100021'
intvolume: ' 34'
isi: 1
issue: 1B
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2208.12206
month: '02'
oa: 1
oa_version: Preprint
page: 1623-1662
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Annals of Applied Probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extremal statistics of quadratic forms of GOE/GUE eigenvectors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2024'
...
---
APC_amount: 2792,52 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15033'
abstract:
- lang: eng
text: The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF)
is among the best studied trafficking regulators in plants, playing crucial and
unique developmental roles in patterning and polarity. The current models place
GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at
the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis
(CME). The mechanistic basis of the developmental function of GN, distinct from
the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains
elusive. Insights from this study largely extend the current notions of GN function.
We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures
distinct from clathrin-coated pits, while CME and secretion proceed normally in
gn knockouts. The functional GN mutant variant GNfewerroots,
absent from the GA, suggests that the cell periphery is the major site of GN action
responsible for its developmental function. Following inhibition by Brefeldin
A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting
selective molecular associations en route to the cell periphery. A study of GN-GNL1
chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN
function in a partially redundant manner. Together, this study offers significant
steps toward the elucidation of the mechanism underlying unique cellular and development
functions of GNOM.
acknowledgement: The authors would like to gratefully acknowledge Dr Xixi Zhang for
cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research
Council Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25
to Jiří Friml
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM
ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993
apa: Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning
function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.68993
chicago: Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning
Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife
Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.
ieee: M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.
mla: Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF
Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications,
2024, doi:10.7554/elife.68993.
short: M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).
corr_author: '1'
date_created: 2024-02-27T07:10:11Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2025-10-15T06:31:47Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.7554/elife.68993
ec_funded: 1
external_id:
isi:
- '001174278000001'
pmid:
- '38381485'
file:
- access_level: open_access
checksum: b2b2d583b433823af731842f1420113e
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:51:50Z
date_updated: 2024-07-22T11:51:50Z
file_id: '17310'
file_name: 2024_eLife_Adamowski.pdf
file_size: 15675744
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:51:50Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2024'
...
---
_id: '15045'
abstract:
- lang: eng
text: Coupling of orbital motion to a spin degree of freedom gives rise to various
transport phenomena in quantum systems that are beyond the standard paradigms
of classical physics. Here, we discuss features of spin-orbit dynamics that can
be visualized using a classical model with two coupled angular degrees of freedom.
Specifically, we demonstrate classical ‘spin’ filtering through our model and
show that the interplay between angular degrees of freedom and dissipation can
lead to asymmetric ‘spin’ transport.
acknowledgement: "We thank Mikhail Lemeshko and members of his group for many inspiring
discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding
provided by Institute of Science and Technology (IST Austria)."
article_number: '12'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees
of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x
apa: Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering
with two degrees of freedom and dissipation. Few-Body Systems. Springer
Nature. https://doi.org/10.1007/s00601-024-01880-x
chicago: Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’
Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems.
Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.
ieee: A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with
two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer
Nature, 2024.
ista: Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with
two degrees of freedom and dissipation. Few-Body Systems. 65, 12.
mla: Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom
and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024,
doi:10.1007/s00601-024-01880-x.
short: A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).
corr_author: '1'
date_created: 2024-03-01T11:39:33Z
date_published: 2024-02-17T00:00:00Z
date_updated: 2025-09-04T12:09:29Z
day: '17'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1007/s00601-024-01880-x
external_id:
arxiv:
- '2401.08454'
isi:
- '001163768200001'
file:
- access_level: open_access
checksum: c4e08cc7bc756da69b1b36fda7bb92fb
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:07:10Z
date_updated: 2024-03-04T07:07:10Z
file_id: '15049'
file_name: 2024_FewBodySys_Varshney.pdf
file_size: 436712
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:07:10Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
keyword:
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Few-Body Systems
publication_identifier:
issn:
- 1432-5411
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Classical ‘spin’ filtering with two degrees of freedom and dissipation
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 65
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15047'
abstract:
- lang: eng
text: Tropical precipitation extremes and their changes with surface warming are
investigated using global storm resolving simulations and high-resolution observations.
The simulations demonstrate that the mesoscale organization of convection, a process
that cannot be physically represented by conventional global climate models, is
important for the variations of tropical daily accumulated precipitation extremes.
In both the simulations and observations, daily precipitation extremes increase
in a more organized state, in association with larger, but less frequent, storms.
Repeating the simulations for a warmer climate results in a robust increase in
monthly-mean daily precipitation extremes. Higher precipitation percentiles have
a greater sensitivity to convective organization, which is predicted to increase
with warming. Without changes in organization, the strongest daily precipitation
extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron
(CC) scaling. Thus, in a future warmer state with increased organization, the
strongest daily precipitation extremes over oceans increase at a faster rate than
CC scaling.
acknowledgement: This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly
appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and
the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the
NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470).
ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no.
01LP1927A) which is supported from German Federal Ministry of Education and Research
(BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant (grant agreement
no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant
agreement no. 101003470). C.M. gratefully acknowledges funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (Project CLUSTER, grant agreement no. 805041).
article_number: eadj6801
article_processing_charge: Yes
article_type: original
author:
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
- first_name: Bjorn
full_name: Stevens, Bjorn
last_name: Stevens
- first_name: Lukas
full_name: Kluft, Lukas
last_name: Kluft
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation
extremes from more organized convection. Science Advances. 2024;10(8).
doi:10.1126/sciadv.adj6801
apa: Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification
of daily tropical precipitation extremes from more organized convection. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801
chicago: Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification
of Daily Tropical Precipitation Extremes from More Organized Convection.” Science
Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.
ieee: J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily
tropical precipitation extremes from more organized convection,” Science Advances,
vol. 10, no. 8. American Association for the Advancement of Science, 2024.
ista: Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical
precipitation extremes from more organized convection. Science Advances. 10(8),
eadj6801.
mla: Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes
from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801,
American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.
short: J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).
date_created: 2024-03-03T23:00:50Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2025-09-04T12:11:18Z
day: '23'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1126/sciadv.adj6801
ec_funded: 1
external_id:
isi:
- '001300045100007'
pmid:
- '38394192'
file:
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creator: dernst
date_created: 2024-03-04T07:34:00Z
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file_name: 2024_ScienceAdv_Bao.pdf
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month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/
scopus_import: '1'
status: public
title: Intensification of daily tropical precipitation extremes from more organized
convection
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2024'
...
---
_id: '15048'
abstract:
- lang: eng
text: Embryogenesis results from the coordinated activities of different signaling
pathways controlling cell fate specification and morphogenesis. In vertebrate
gastrulation, both Nodal and BMP signaling play key roles in germ layer specification
and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis
is still insufficiently understood. Here, we took a reductionist approach using
zebrafish embryonic explants to study the coordination of Nodal and BMP signaling
for embryo patterning and morphogenesis. We show that Nodal signaling triggers
explant elongation by inducing mesendodermal progenitors but also suppressing
BMP signaling activity at the site of mesendoderm induction. Consistent with this,
ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm
intercalations, key processes during explant elongation. Translating these ex
vivo observations to the intact embryo showed that, similar to explants, Nodal
signaling suppresses the effect of BMP signaling on cell intercalations in the
dorsal domain, thus allowing robust embryonic axis elongation. These findings
suggest a dual function of Nodal signaling in embryonic axis elongation by both
inducing mesendoderm and suppressing BMP effects in the dorsal portion of the
mesendoderm.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Patrick Müller for sharing the chordintt250 mutant zebrafish
line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b
plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated
the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro
and Katherine Rogers and members of the Heisenberg lab for discussions, technical
advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo
for discussions. We thank the Imaging and Optics Facility as well as the Life Science
facility at IST Austria for support with microscopy and fish maintenance.\r\nThis
work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573
to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy
of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience
and Technology Austria. "
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation
by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18.
doi:10.1242/dev.202316
apa: Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J.
(2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling.
Development. The Company of Biologists. https://doi.org/10.1242/dev.202316
chicago: Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp
J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.”
Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.
ieee: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust
axis elongation by Nodal-dependent restriction of BMP signaling,” Development,
vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.
ista: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis
elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4),
1–18.
mla: Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction
of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists,
2024, pp. 1–18, doi:10.1242/dev.202316.
short: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development
151 (2024) 1–18.
corr_author: '1'
date_created: 2024-03-03T23:00:50Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-09-04T12:10:40Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1242/dev.202316
ec_funded: 1
external_id:
isi:
- '001170580200001'
pmid:
- '38372390'
file:
- access_level: open_access
checksum: 6961ea10012bf0d266681f9628bb8f13
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:24:43Z
date_updated: 2024-03-04T07:24:43Z
file_id: '15050'
file_name: 2024_Development_Schauer.pdf
file_size: 14839986
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:24:43Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1-18
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14926'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Robust axis elongation by Nodal-dependent restriction of BMP 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 151
year: '2024'
...