---
_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
license: https://creativecommons.org/licenses/by/4.0/
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:
- access_level: open_access
checksum: d4ec4f05a6d14745057e14d1b8bf45ae
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:34:00Z
date_updated: 2024-03-04T07:34:00Z
file_id: '15051'
file_name: 2024_ScienceAdv_Bao.pdf
file_size: 800926
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:34:00Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '8'
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'
- _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'
...
---
DOAJ_listed: '1'
_id: '15053'
abstract:
- lang: eng
text: Atom-based quantum simulators have had many successes in tackling challenging
quantum many-body problems, owing to the precise and dynamical control that they
provide over the systems' parameters. They are, however, often optimized to address
a specific type of problem. Here, we present the design and implementation of
a 6Li-based quantum gas platform that provides wide-ranging capabilities and is
able to address a variety of quantum many-body problems. Our two-chamber architecture
relies on a robust combination of gray molasses and optical transport from a laser-cooling
chamber to a glass cell with excellent optical access. There, we first create
unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap
and characterize them using in situ thermometry, reaching temperatures below 20
nK. This allows us to enter the deep superfluid regime with samples of extreme
diluteness, where the interparticle spacing is sufficiently large for direct single-atom
imaging. Second, we generate optical lattice potentials with triangular and honeycomb
geometry in which we study diffraction of molecular Bose-Einstein condensates,
and show how going beyond the Kapitza-Dirac regime allows us to unambiguously
distinguish between the two geometries. With the ability to probe quantum many-body
physics in both discrete and continuous space, and its suitability for bulk and
single-atom imaging, our setup represents an important step towards achieving
a wide-scope quantum simulator.
acknowledgement: We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel,
Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance
in the early stages of this project, and Sebastian Will for a critical reading of
the manuscript. This work has been supported by Agence Nationale de la Recherche
(Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159),
CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ
(Super2D and SISCo) and DIM QuanTiP.
article_number: '013158'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Shuwei
full_name: Jin, Shuwei
last_name: Jin
- first_name: Kunlun
full_name: Dai, Kunlun
last_name: Dai
- first_name: Joris
full_name: Verstraten, Joris
last_name: Verstraten
- first_name: Maxime
full_name: Dixmerias, Maxime
last_name: Dixmerias
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Christophe
full_name: Salomon, Christophe
last_name: Salomon
- first_name: Bruno
full_name: Peaudecerf, Bruno
last_name: Peaudecerf
- first_name: Tim
full_name: de Jongh, Tim
last_name: de Jongh
- first_name: Tarik
full_name: Yefsah, Tarik
last_name: Yefsah
citation:
ama: Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum
simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158
apa: Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C.,
… Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical
Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158
chicago: Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al
Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose
Platform for Analog Quantum Simulation.” Physical Review Research. American
Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.
ieee: S. Jin et al., “Multipurpose platform for analog quantum simulation,”
Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.
ista: Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf
B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation.
Physical Review Research. 6(1), 013158.
mla: Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.”
Physical Review Research, vol. 6, no. 1, 013158, American Physical Society,
2024, doi:10.1103/physrevresearch.6.013158.
short: S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B.
Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).
date_created: 2024-03-04T07:42:52Z
date_published: 2024-02-13T00:00:00Z
date_updated: 2025-05-14T09:32:25Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.6.013158
external_id:
arxiv:
- '2304.08433'
file:
- access_level: open_access
checksum: ba2ae3e3a011f8897d3803c9366a67e2
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:53:08Z
date_updated: 2024-03-04T07:53:08Z
file_id: '15054'
file_name: 2024_PhysicalReviewResearch_Jin.pdf
file_size: 4025988
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:53:08Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
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: Multipurpose platform for analog quantum simulation
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'
...
---
APC_amount: 3041,76 EUR
OA_place: publisher
OA_type: hybrid
_id: '15083'
abstract:
- lang: eng
text: 'Direct reciprocity is a powerful mechanism for cooperation in social dilemmas.
The very logic of reciprocity, however, seems to require that individuals are
symmetric, and that everyone has the same means to influence each others’ payoffs.
Yet in many applications, individuals are asymmetric. Herein, we study the effect
of asymmetry in linear public good games. Individuals may differ in their endowments
(their ability to contribute to a public good) and in their productivities (how
effective their contributions are). Given the individuals’ productivities, we
ask which allocation of endowments is optimal for cooperation. To this end, we
consider two notions of optimality. The first notion focuses on the resilience
of cooperation. The respective endowment distribution ensures that full cooperation
is feasible even under the most adverse conditions. The second notion focuses
on efficiency. The corresponding endowment distribution maximizes group welfare.
Using analytical methods, we fully characterize these two endowment distributions.
This analysis reveals that both optimality notions favor some endowment inequality:
More productive players ought to get higher endowments. Yet the two notions disagree
on how unequal endowments are supposed to be. A focus on resilience results in
less inequality. With additional simulations, we show that the optimal endowment
allocation needs to account for both the resilience and the efficiency of cooperation.'
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale
de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010)
(to M.K.).'
article_number: e2315558121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Valentin
full_name: Hübner, Valentin
id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910
last_name: Hübner
orcid: 0009-0001-5009-4987
- first_name: Manuel
full_name: Staab, Manuel
last_name: Staab
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Maria
full_name: Kleshnina, Maria
last_name: Kleshnina
citation:
ama: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience
of cooperation in asymmetric social dilemmas. Proceedings of the National Academy
of Sciences of the United States of America. 2024;121(10). doi:10.1073/pnas.2315558121
apa: Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024).
Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2315558121
chicago: Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee,
and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social
Dilemmas.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.
ieee: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency
and resilience of cooperation in asymmetric social dilemmas,” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 10. National Academy of Sciences, 2024.
ista: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and
resilience of cooperation in asymmetric social dilemmas. Proceedings of the National
Academy of Sciences of the United States of America. 121(10), e2315558121.
mla: Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric
Social Dilemmas.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 121, no. 10, e2315558121, National Academy of Sciences,
2024, doi:10.1073/pnas.2315558121.
short: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of
the National Academy of Sciences of the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-03-05T09:18:49Z
date_published: 2024-03-05T00:00:00Z
date_updated: 2026-04-07T12:30:56Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1073/pnas.2315558121
ec_funded: 1
external_id:
isi:
- '001207786500004'
pmid:
- '38408249'
file:
- access_level: open_access
checksum: 068520e3efd4d008bb9177e8aedb7d22
content_type: application/pdf
creator: dernst
date_created: 2024-03-12T13:12:22Z
date_updated: 2024-03-12T13:12:22Z
file_id: '15109'
file_name: 2024_PNAS_Huebner.pdf
file_size: 2203220
relation: main_file
success: 1
file_date_updated: 2024-03-12T13:12:22Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/
record:
- id: '15108'
relation: research_data
status: public
- id: '19903'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Efficiency and resilience of cooperation in asymmetric social dilemmas
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: '15093'
abstract:
- lang: eng
text: We present a dynamic data structure for maintaining the persistent homology
of a time series of real numbers. The data structure supports local operations,
including the insertion and deletion of an item and the cutting and concatenating
of lists, each in time O(log n + k), in which n counts the critical items and
k the changes in the augmented persistence diagram. To achieve this, we design
a tailor-made tree structure with an unconventional representation, referred to
as banana tree, which may be useful in its own right.
acknowledgement: The first and second authors are funded by the European Research Council under the
European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha
Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31,
and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The
third author received funding by the European Research Council under the European
Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures
(MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize
with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant
no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The
fourth author is funded by the Vienna Graduate School on Computational Optimization,
FWF project no. W1260-N35.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- 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: Lara
full_name: Ost, Lara
last_name: Ost
citation:
ama: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. Dynamically maintaining
the persistent homology of time series. In: Woodruff DP, ed. Proceedings of
the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society
for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11'
apa: 'Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M., & Ost, L.
(2024). Dynamically maintaining the persistent homology of time series. In D.
P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11'
chicago: Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika Henzinger,
and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.”
In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied
Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.
ieee: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, and L. Ost, “Dynamically
maintaining the persistent homology of time series,” in Proceedings of the
2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria,
VA, USA, 2024, pp. 243–295.
ista: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. 2024. Dynamically
maintaining the persistent homology of time series. Proceedings of the 2024 Annual
ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete
Algorithms, 243–295.'
mla: Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent
Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium
on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial
and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.
short: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, L. Ost, in:, D.P.
Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.
conference:
end_date: 2024-01-10
location: Alexandria, VA, USA
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2024-01-07
corr_author: '1'
date_created: 2024-03-08T10:27:39Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '04'
department:
- _id: HeEd
- _id: MoHe
doi: 10.1137/1.9781611977912.11
ec_funded: 1
editor:
- first_name: David P.
full_name: Woodruff, David P.
last_name: Woodruff
external_id:
arxiv:
- '2311.01115'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2311.01115
month: '01'
oa: 1
oa_version: Preprint
page: 243 - 295
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
- _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: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA)
publication_identifier:
eisbn:
- '9781611977912'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '15094'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamically maintaining the persistent homology of time series
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '15094'
abstract:
- lang: eng
text: "Point sets, geometric networks, and arrangements of hyperplanes are fundamental
objects in\r\ndiscrete geometry that have captivated mathematicians for centuries,
if not millennia. This\r\nthesis seeks to cast new light on these structures by
illustrating specific instances where a\r\ntopological perspective, specifically
through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt
first glance, the topology of these geometric objects might seem uneventful: point
sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition
of Rd, which\r\nis a contractible space, and the topology of a network primarily
involves the enumeration\r\nof connected components and cycles within the network.
However, beneath this apparent\r\nsimplicity, there lies an array of intriguing
structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused
on three case studies, each addressing one of the mentioned objects, this work\r\nwill
showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry,
algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
citation:
ama: Cultrera di Montesano S. Persistence and Morse theory for discrete geometric
structures. 2024. doi:10.15479/at:ista:15094
apa: Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete
geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094
chicago: Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete
Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.
ieee: S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric
structures,” Institute of Science and Technology Austria, 2024.
ista: Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric
structures. Institute of Science and Technology Austria.
mla: Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete
Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.
short: S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric
Structures, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-03-08T15:28:10Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2026-04-07T12:58:48Z
day: '08'
ddc:
- '514'
- '500'
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:15094
ec_funded: 1
file:
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creator: scultrer
date_created: 2024-03-14T08:55:07Z
date_updated: 2024-03-14T08:55:07Z
file_id: '15112'
file_name: Thesis Sebastiano.pdf
file_size: 4106872
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month: '03'
oa: 1
oa_version: Published Version
page: '108'
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
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '15091'
relation: part_of_dissertation
status: public
- id: '11660'
relation: part_of_dissertation
status: public
- id: '15090'
relation: part_of_dissertation
status: public
- id: '15093'
relation: part_of_dissertation
status: public
- id: '13182'
relation: part_of_dissertation
status: public
- id: '11658'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Persistence and Morse theory for discrete geometric structures
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
_id: '15097'
abstract:
- lang: eng
text: Global storm-resolving models (GSRMs) use strongly refined horizontal grids
compared with the climate models typically used in the Coupled Model Intercomparison
Project (CMIP) but employ comparable vertical grid spacings. Here, we study how
changes in the vertical grid spacing and adjustments to the integration time step
affect the basic climate quantities simulated by the ICON-Sapphire atmospheric
GSRM. Simulations are performed over a 45 d period for five different vertical
grids with between 55 and 540 vertical layers and maximum tropospheric vertical
grid spacings of between 800 and 50 m, respectively. The effects of changes in
the vertical grid spacing are compared with the effects of reducing the horizontal
grid spacing from 5 to 2.5 km. For most of the quantities considered, halving
the vertical grid spacing has a smaller effect than halving the horizontal grid
spacing, but it is not negligible. Each halving of the vertical grid spacing,
along with the necessary reductions in time step length, increases cloud liquid
water by about 7 %, compared with an approximate 16 % decrease for halving the
horizontal grid spacing. The effect is due to both the vertical grid refinement
and the time step reduction. There is no tendency toward convergence in the range
of grid spacings tested here. The cloud ice amount also increases with a refinement
in the vertical grid, but it is hardly affected by the time step length and does
show a tendency to converge. While the effect on shortwave radiation is globally
dominated by the altered reflection due to the change in the cloud liquid water
content, the effect on longwave radiation is more difficult to interpret because
changes in the cloud ice concentration and cloud fraction are anticorrelated in
some regions. The simulations show that using a maximum tropospheric vertical
grid spacing larger than 400 m would increase the truncation error strongly. Computing
time investments in a further vertical grid refinement can affect the truncation
errors of GSRMs similarly to comparable investments in horizontal refinement,
because halving the vertical grid spacing is generally cheaper than halving the
horizontal grid spacing. However, convergence of boundary layer cloud properties
cannot be expected, even for the smallest maximum tropospheric grid spacing of
50 m used in this study.
acknowledgement: "The authors wish to thank Ann Kristin Naumann and three anonymous
reviewers for very helpful comments on an earlier version of this paper. We are
grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding
running the simulations. We thank Luis Kornblueh for providing an external vertical
grid generator and resolving the memory requirements for the very fine vertical
grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations
were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff
for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial
support from the SOCTOC project within the framework of the ROMIC program, funded
by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe
article processing charges for this open-access publication were covered by the
Max Planck Society."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hauke
full_name: Schmidt, Hauke
last_name: Schmidt
- first_name: Sebastian
full_name: Rast, Sebastian
last_name: Rast
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
- first_name: Amrit
full_name: Cassim, Amrit
last_name: Cassim
- first_name: Shih Wei
full_name: Fang, Shih Wei
last_name: Fang
- first_name: Diego
full_name: Jimenez-De La Cuesta, Diego
last_name: Jimenez-De La Cuesta
- first_name: Paul
full_name: Keil, Paul
last_name: Keil
- first_name: Lukas
full_name: Kluft, Lukas
last_name: Kluft
- first_name: Clarissa
full_name: Kroll, Clarissa
last_name: Kroll
- first_name: Theresa
full_name: Lang, Theresa
last_name: Lang
- first_name: Ulrike
full_name: Niemeier, Ulrike
last_name: Niemeier
- first_name: Andrea
full_name: Schneidereit, Andrea
last_name: Schneidereit
- first_name: Andrew I.L.
full_name: Williams, Andrew I.L.
last_name: Williams
- first_name: Bjorn
full_name: Stevens, Bjorn
last_name: Stevens
citation:
ama: Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate
simulated in the ICON-Sapphire global storm-resolving model. Geoscientific
Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024
apa: Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta,
D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated
in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development.
European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024
chicago: Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang,
Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing
on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific
Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.
ieee: H. Schmidt et al., “Effects of vertical grid spacing on the climate
simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific
Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584,
2024.
ista: Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil
P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens
B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire
global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.
mla: Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated
in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development,
vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.
short: H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta,
P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams,
B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.
date_created: 2024-03-10T23:00:53Z
date_published: 2024-02-22T00:00:00Z
date_updated: 2025-09-04T12:17:17Z
day: '22'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5194/gmd-17-1563-2024
external_id:
isi:
- '001190535000001'
file:
- access_level: open_access
checksum: 270d2340402729b0532f7072ea914cae
content_type: application/pdf
creator: dernst
date_created: 2024-03-13T08:59:21Z
date_updated: 2024-03-13T08:59:21Z
file_id: '15111'
file_name: 2024_GeoscientificModelDev_Schmidt.pdf
file_size: 13364601
relation: main_file
success: 1
file_date_updated: 2024-03-13T08:59:21Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1563-1584
publication: Geoscientific Model Development
publication_identifier:
eissn:
- 1991-9603
issn:
- 1991-959X
publication_status: published
publisher: European Geosciences Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire
global storm-resolving model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15098'
abstract:
- lang: eng
text: The paper is devoted to the analysis of the global well-posedness and the
interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic
boundary conditions. The noise, white in time and coloured in space, can be interpreted
as the physical law describing the driving mechanism on the atmosphere–ocean interface,
i.e. as a balance of the shear stress of the ocean and the horizontal wind force.
acknowledgement: The authors thank Professor Franco Flandoli for useful discussions
and valuable insight into the subject. In particular, A.A. would like to thank professor
Franco Flandoli for hosting and financially contributing to his research visit at
Scuola Normale di Pisa in January 2023, where this work started. E.L. would like
to express sincere gratitude to Professor Marco Fuhrman for igniting his interest
in this particular field of research. E.L. want to thank Professor Matthias Hieber
and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous
referee for helpful comments which improved the paper from its initial version.Open
access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement.
A. Agresti has received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant Agreement
No. 948819).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Eliseo
full_name: Luongo, Eliseo
last_name: Luongo
citation:
ama: Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes
equations with stochastic boundary conditions. Mathematische Annalen. 2024;390:2727-2766.
doi:10.1007/s00208-024-02812-0
apa: Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity
of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische
Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0
chicago: Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior
Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.”
Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.
ieee: A. Agresti and E. Luongo, “Global well-posedness and interior regularity of
2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische
Annalen, vol. 390. Springer Nature, pp. 2727–2766, 2024.
ista: Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of
2D Navier-Stokes equations with stochastic boundary conditions. Mathematische
Annalen. 390, 2727–2766.
mla: Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity
of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische
Annalen, vol. 390, Springer Nature, 2024, pp. 2727–66, doi:10.1007/s00208-024-02812-0.
short: A. Agresti, E. Luongo, Mathematische Annalen 390 (2024) 2727–2766.
date_created: 2024-03-10T23:00:54Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-04T12:19:59Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00208-024-02812-0
ec_funded: 1
external_id:
arxiv:
- '2306.11081'
isi:
- '001172711400002'
pmid:
- '39351582'
file:
- access_level: open_access
checksum: d55cac8bddea09a97f06612825c4f229
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T08:23:36Z
date_updated: 2025-01-09T08:23:36Z
file_id: '18790'
file_name: 2024_MathAnnalen_Agresti.pdf
file_size: 661557
relation: main_file
success: 1
file_date_updated: 2025-01-09T08:23:36Z
has_accepted_license: '1'
intvolume: ' 390'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2727-2766
pmid: 1
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Mathematische Annalen
publication_identifier:
eissn:
- 1432-1807
issn:
- 0025-5831
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global well-posedness and interior regularity of 2D Navier-Stokes equations
with stochastic boundary conditions
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: 390
year: '2024'
...
---
_id: '15099'
abstract:
- lang: eng
text: Speciation is a key evolutionary process that is not yet fully understood.
Combining population genomic and ecological data from multiple diverging pairs
of marine snails (Littorina) supports the search for speciation mechanisms. Placing
pairs on a one-dimensional speciation continuum, from undifferentiated populations
to species, obscured the complexity of speciation. Adding multiple axes helped
to describe either speciation routes or reproductive isolation in the snails.
Divergent ecological selection repeatedly generated barriers between ecotypes,
but appeared less important in completing speciation while genetic incompatibilities
played a key role. Chromosomal inversions contributed to genomic barriers, but
with variable impact. A multidimensional (hypercube) approach supported framing
of questions and identification of knowledge gaps and can be useful to understand
speciation in many other systems.
acknowledgement: KJ, MR, and RKB were supported by grants from the Swedish Research
Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported
by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation
(PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council
RCN (Project number 315287). We thank the members of the Integration of Speciation
Research network for stimulating discussions, the Littorina research community for
important contributions of data and analyses, and Cynthia Riginos for useful comments
on an earlier draft.
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed
by marine snails. Trends in Genetics. 2024;40(4):337-351. doi:10.1016/j.tig.2024.01.002
apa: Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin,
R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by
marine snails. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2024.01.002
chicago: Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja
M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation
Revealed by Marine Snails.” Trends in Genetics. Elsevier, 2024. https://doi.org/10.1016/j.tig.2024.01.002.
ieee: K. Johannesson et al., “Diverse pathways to speciation revealed by
marine snails,” Trends in Genetics, vol. 40, no. 4. Elsevier, pp. 337–351,
2024.
ista: Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski
S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.
40(4), 337–351.
mla: Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine
Snails.” Trends in Genetics, vol. 40, no. 4, Elsevier, 2024, pp. 337–51,
doi:10.1016/j.tig.2024.01.002.
short: K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin,
S. Stankowski, Trends in Genetics 40 (2024) 337–351.
date_created: 2024-03-10T23:00:54Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-09-04T12:18:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tig.2024.01.002
external_id:
isi:
- '001224671300001'
pmid:
- '38395682'
file:
- access_level: open_access
checksum: 3077ea808c4cdc24d02dc58aced7eb35
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T12:05:58Z
date_updated: 2024-07-22T12:05:58Z
file_id: '17313'
file_name: 2024_TrendsGenetics_Johannesson.pdf
file_size: 2288340
relation: main_file
success: 1
file_date_updated: 2024-07-22T12:05:58Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 337-351
pmid: 1
publication: Trends in Genetics
publication_identifier:
eissn:
- 1362-4555
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diverse pathways to speciation revealed by marine snails
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: 40
year: '2024'
...
---
_id: '15108'
abstract:
- lang: eng
text: "in the research article \"Efficiency and resilience of cooperation in asymmetric
social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu
Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for
the case of two and three players, both described below."
article_processing_charge: No
author:
- first_name: Valentin
full_name: Hübner, Valentin
id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910
last_name: Hübner
orcid: 0009-0001-5009-4987
- first_name: Maria
full_name: Kleshnina, Maria
last_name: Kleshnina
citation:
ama: Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation
in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167
apa: Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience
of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167
chicago: Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and
Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.
ieee: V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience
of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.
ista: Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience
of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.
mla: Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and
Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.
short: V. Hübner, M. Kleshnina, (2024).
corr_author: '1'
date_created: 2024-03-12T13:02:58Z
date_published: 2024-02-09T00:00:00Z
date_updated: 2025-09-04T12:14:54Z
day: '09'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.5281/ZENODO.10639167
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://10.5281/zenodo.10639167
month: '02'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '15083'
relation: used_in_publication
status: public
status: public
title: Computer code for "Efficiency and resilience of cooperation in asymmetric social
dilemmas"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_type: free access
_id: '15114'
abstract:
- lang: eng
text: As a key liquid organic hydrogen carrier, investigating the decomposition
of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative
for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms
and key intermediates involved in the dehydrogenation process of formic acid remain
a great topic of debate due to ambiguous adsorbate interactions. In this research,
we develop an advanced microkinetic model based on first-principles calculations,
accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive
mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage
effects in formic acid dehydrogenation. Our findings unequivocally demonstrate
that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible
to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental
results, the selectivity of H2 in the decomposition of formic acid on the Pd (1
1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic
analysis aligns perfectly with experimental values at a temperature of 373 K.
acknowledgement: The authors acknowledge the financial support from the National Key
Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the
National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation
Team (2017R5203).
article_number: '119959'
article_processing_charge: No
article_type: original
author:
- first_name: Zihao
full_name: Yao, Zihao
last_name: Yao
- first_name: Xu
full_name: Liu, Xu
last_name: Liu
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: Jianguo
full_name: Wang, Jianguo
last_name: Wang
citation:
ama: 'Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2
production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959'
apa: 'Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction
mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent
microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959'
chicago: 'Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction
Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent
Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.'
ieee: 'Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism
for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.'
ista: 'Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism
for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling. Chemical Engineering Science. 291, 119959.'
mla: 'Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via
Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.”
Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.'
short: Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).
date_created: 2024-03-17T23:00:57Z
date_published: 2024-06-05T00:00:00Z
date_updated: 2025-09-04T13:02:40Z
day: '05'
department:
- _id: MaIb
doi: 10.1016/j.ces.2024.119959
external_id:
isi:
- '001203872000001'
intvolume: ' 291'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ces.2024.119959
month: '06'
oa: 1
oa_version: None
publication: Chemical Engineering Science
publication_identifier:
issn:
- 0009-2509
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unravelling the reaction mechanism for H2 production via formic acid decomposition
over Pd: Coverage-dependent microkinetic modeling'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 291
year: '2024'
...
---
_id: '15116'
abstract:
- lang: eng
text: Water is known to play an important role in collagen self-assembly, but it
is still largely unclear how water–collagen interactions influence the assembly
process and determine the fibril network properties. Here, we use the H2O/D2O
isotope effect on the hydrogen-bond strength in water to investigate the role
of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and
compare the growth kinetics and the structure of the collagen assemblies formed
in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster
in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils,
that form a more inhomogeneous and softer network, with a fourfold reduction in
elastic modulus when compared to H2O. Combining spectroscopic measurements with
atomistic simulations, we show that collagen in D2O is less hydrated than in H2O.
This partial dehydration lowers the enthalpic penalty for water removal and reorganization
at the collagen–water interface, increasing the self-assembly rate and the number
of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained
simulations show that the acceleration in the initial nucleation rate can be reproduced
by the enhancement of electrostatic interactions. These results show that water
acts as a mediator between collagen monomers, by modulating their interactions
so as to optimize the assembly process and, thus, the final network properties.
We believe that isotopically modulating the hydration of proteins can be a valuable
method to investigate the role of water in protein structural dynamics and protein
self-assembly.
acknowledgement: We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla,
and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the
useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical
support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic
Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education,
Culture and Science (OCW) and The Netherlands Organization for Scientific Research
and from NWO grant OCENW.GROOT.2019.022. This work has received support from the
National Research Foundation of Korea (NRF), funded by the Ministry of Science and
ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project
(with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme
Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges
support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia
Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from
Royal Society and European Research Council Starting Grant. G. Giubertoni kindly
thanks to the Care4Bones community and the Collagen Café community for reminding
that we do not own the knowledge we create, but it is, rather, a collective resource
intended for the advancement of human progress.
article_number: e2313162121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Giulia
full_name: Giubertoni, Giulia
last_name: Giubertoni
- first_name: Liru
full_name: Feng, Liru
last_name: Feng
- first_name: Kevin
full_name: Klein, Kevin
last_name: Klein
- first_name: Guido
full_name: Giannetti, Guido
last_name: Giannetti
- first_name: Luco
full_name: Rutten, Luco
last_name: Rutten
- first_name: Yeji
full_name: Choi, Yeji
last_name: Choi
- first_name: Anouk
full_name: Van Der Net, Anouk
last_name: Van Der Net
- first_name: Gerard
full_name: Castro-Linares, Gerard
last_name: Castro-Linares
- first_name: Federico
full_name: Caporaletti, Federico
last_name: Caporaletti
- first_name: Dimitra
full_name: Micha, Dimitra
last_name: Micha
- first_name: Johannes
full_name: Hunger, Johannes
last_name: Hunger
- first_name: Antoine
full_name: Deblais, Antoine
last_name: Deblais
- first_name: Daniel
full_name: Bonn, Daniel
last_name: Bonn
- first_name: Nico
full_name: Sommerdijk, Nico
last_name: Sommerdijk
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ioana M.
full_name: Ilie, Ioana M.
last_name: Ilie
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Sander
full_name: Woutersen, Sander
last_name: Woutersen
citation:
ama: Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen
self-assembly by isotopically modulating collagen hydration. Proceedings of
the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2313162121
apa: Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., …
Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2313162121
chicago: Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten,
Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen
Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.
ieee: G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11. National
Academy of Sciences, 2024.
ista: Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net
A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk
N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of
water in collagen self-assembly by isotopically modulating collagen hydration.
Proceedings of the National Academy of Sciences of the United States of America.
121(11), e2313162121.
mla: Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly
by Isotopically Modulating Collagen Hydration.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.
short: G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van
Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D.
Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings
of the National Academy of Sciences of the United States of America 121 (2024).
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2025-09-04T13:03:56Z
day: '12'
ddc:
- '550'
department:
- _id: AnSa
doi: 10.1073/pnas.2313162121
external_id:
isi:
- '001206387400001'
pmid:
- '38451946'
file:
- access_level: open_access
checksum: a3f7fdc29dd9f0a38952ab4e322b3a05
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T10:22:42Z
date_updated: 2024-03-19T10:22:42Z
file_id: '15125'
file_name: 2024_PNAS_Giubertoni.pdf
file_size: 12952586
relation: main_file
success: 1
file_date_updated: 2024-03-19T10:22:42Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15126'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Elucidating the role of water in collagen self-assembly by isotopically modulating
collagen hydration
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: 121
year: '2024'
...
---
_id: '15117'
abstract:
- lang: eng
text: 'The hippocampal mossy fiber synapse, formed between axons of dentate gyrus
granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the
trisynaptic circuitry of the hippocampus. Because of its comparatively large size,
this synapse is accessible to direct presynaptic recording, allowing a rigorous
investigation of the biophysical mechanisms of synaptic transmission and plasticity.
Furthermore, because of its placement in the very center of the hippocampal memory
circuit, this synapse seems to be critically involved in several higher network
functions, such as learning, memory, pattern separation, and pattern completion.
Recent work based on new technologies in both nanoanatomy and nanophysiology,
including presynaptic patch-clamp recording, paired recording, super-resolution
light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy,
has provided new insights into the structure, biophysics, and network function
of this intriguing synapse. This brings us one step closer to answering a fundamental
question in neuroscience: how basic synaptic properties shape higher network computations.'
acknowledgement: "We thank previous students, postdocs, and collaborators, particularly
J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane,
D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li,
K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston,
and N. Vyleta for their outstanding experimental contributions. We also thank P.
Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically
reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and
L. Slomianka for useful discussions. We apologize that, due to space constraints,
not all relevant papers could be cited.\r\nThis project was supported by the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone
grant), both to P.J."
article_processing_charge: No
article_type: review
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant”
cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757
apa: Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit
function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757
chicago: Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit
Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024.
https://doi.org/10.1126/science.adg6757.
ieee: D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function
of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687.
AAAS, p. eadg6757, 2024.
ista: Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of
a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.
mla: Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit
Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383,
no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.
short: D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.
corr_author: '1'
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2025-09-04T13:04:34Z
day: '08'
department:
- _id: PeJo
doi: 10.1126/science.adg6757
ec_funded: 1
external_id:
isi:
- '001216996700015'
pmid:
- '38452088'
intvolume: ' 383'
isi: 1
issue: '6687'
language:
- iso: eng
month: '03'
oa_version: None
page: eadg6757
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure, biophysics, and circuit function of a "giant" cortical presynaptic
terminal
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 383
year: '2024'
...
---
_id: '15118'
abstract:
- lang: eng
text: Cell division in all domains of life requires the orchestration of many proteins,
but in Archaea most of the machinery remains poorly characterized. Here we investigate
the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins
containing photosynthetic reaction centre (PRC) barrel domains that play an essential
role in archaeal cell division. We rename these proteins cell division protein
B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause
severe cell division defects, generating drastically enlarged cells. Fluorescence
microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed
an unusually disordered divisome that is not organized into a distinct ring-like
structure. Biochemical analysis shows that SepF forms a tripartite complex with
CdpB1/2 and crystal structures suggest that these two proteins might form filaments,
possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results
indicate that PRC-domain proteins play essential roles in FtsZ-based cell division
in Archaea.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid
pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673;
RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from
the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and
support. We thank Scientific Computing at the MRC LMB for their support. We thank
L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support
Facility for help with the SEC coupled with multi-angle light scattering experiments.
We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of
Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported
by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C.
and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number
Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file
reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the
French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative
Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and
the computational and storage services (Maestro cluster) provided by the IT department
at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF)
Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular
Biology has applied a CC BY public copyright licence to any author accepted manuscript
version arising.
article_processing_charge: No
article_type: original
author:
- first_name: Phillip
full_name: Nußbaum, Phillip
last_name: Nußbaum
- first_name: Danguole
full_name: Kureisaite-Ciziene, Danguole
last_name: Kureisaite-Ciziene
- first_name: Dom
full_name: Bellini, Dom
last_name: Bellini
- first_name: Chris
full_name: Van Der Does, Chris
last_name: Van Der Does
- first_name: Marko
full_name: Kojic, Marko
id: 73e7ecd4-dc85-11ea-9058-88a16394b160
last_name: Kojic
orcid: 0000-0001-7244-8128
- first_name: Najwa
full_name: Taib, Najwa
last_name: Taib
- first_name: Anna
full_name: Yeates, Anna
last_name: Yeates
- first_name: Maxime
full_name: Tourte, Maxime
last_name: Tourte
- first_name: Simonetta
full_name: Gribaldo, Simonetta
last_name: Gribaldo
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Sonja Verena
full_name: Albers, Sonja Verena
last_name: Albers
citation:
ama: Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic
reaction centre domains modulate FtsZ-based archaeal cell division. Nature
Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5
apa: Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic,
M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction
centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology.
Springer Nature. https://doi.org/10.1038/s41564-024-01600-5
chicago: Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der
Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic
Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature
Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.
ieee: P. Nußbaum et al., “Proteins containing photosynthetic reaction centre
domains modulate FtsZ-based archaeal cell division,” Nature Microbiology,
vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.
ista: Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib
N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins
containing photosynthetic reaction centre domains modulate FtsZ-based archaeal
cell division. Nature Microbiology. 9(3), 698–711.
mla: Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre
Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology,
vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.
short: P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic,
N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature
Microbiology 9 (2024) 698–711.
date_created: 2024-03-17T23:00:58Z
date_published: 2024-03-04T00:00:00Z
date_updated: 2026-04-07T12:27:57Z
day: '04'
department:
- _id: MaLo
doi: 10.1038/s41564-024-01600-5
external_id:
isi:
- '001183270800021'
pmid:
- '38443575'
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 698-711
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
publication: Nature Microbiology
publication_identifier:
eissn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20741'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Proteins containing photosynthetic reaction centre domains modulate FtsZ-based
archaeal cell division
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15122'
abstract:
- lang: eng
text: Quantum computers are increasing in size and quality but are still very noisy.
Error mitigation extends the size of the quantum circuits that noisy devices can
meaningfully execute. However, state-of-the-art error mitigation methods are hard
to implement and the limited qubit connectivity in superconducting qubit devices
restricts most applications to the hardware's native topology. Here we show a
quantum approximate optimization algorithm (QAOA) on nonplanar random regular
graphs with up to 40 nodes enabled by a machine learning-based error mitigation.
We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward
neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful
parameter optimization for the largest graph which requires running quantum circuits
with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and
not only expectation values, in quantum approximate optimization. These results
are a step towards executing quantum approximate optimization at a scale that
is not classically simulable. Reaching such system sizes is key to properly understanding
the true potential of heuristic algorithms like QAOA.
acknowledgement: S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in
quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and
S. Woerner for fruitful discussions.
article_number: '013223'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Daniel J.
full_name: Egger, Daniel J.
last_name: Egger
citation:
ama: Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research.
2024;6(1). doi:10.1103/PhysRevResearch.6.013223
apa: Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization
on nonplanar graphs with machine learning noise mitigation. Physical Review
Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223
chicago: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.
ieee: S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on
nonplanar graphs with machine learning noise mitigation,” Physical Review Research,
vol. 6, no. 1. American Physical Society, 2024.
ista: Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research. 6(1),
013223.
mla: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.
short: S. Sack, D.J. Egger, Physical Review Research 6 (2024).
corr_author: '1'
date_created: 2024-03-17T23:00:59Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-05-14T09:32:15Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevResearch.6.013223
external_id:
arxiv:
- '2307.14427'
file:
- access_level: open_access
checksum: 274c9f1b15b3547a10a03f39e4ccc582
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T07:16:38Z
date_updated: 2024-03-19T07:16:38Z
file_id: '15123'
file_name: 2024_PhysicalReviewResearch_Sack.pdf
file_size: 2777593
relation: main_file
success: 1
file_date_updated: 2024-03-19T07:16:38Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d
name: IMB PhD Nomination Fellowship - Stefan Sack
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: Large-scale quantum approximate optimization on nonplanar graphs with machine
learning noise mitigation
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'
...
---
_id: '15146'
abstract:
- lang: eng
text: The extracellular matrix (ECM) serves as a scaffold for cells and plays an
essential role in regulating numerous cellular processes, including cell migration
and proliferation. Due to limitations in specimen preparation for conventional
room-temperature electron microscopy, we lack structural knowledge on how ECM
components are secreted, remodeled, and interact with surrounding cells. We have
developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion
beam milling, the lift-out extraction procedure, and cryo-electron tomography.
Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting
in a versatile tool closely mimicking ECM environments. This allows us to visualize
ECM for the first time in its hydrated, native context. Our data reveal an intricate
network of extracellular fibers, their positioning relative to matrix-secreting
cells, and previously unresolved structural entities. Our workflow and results
add to the structural atlas of the ECM, providing novel insights into its secretion
and assembly.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
- _id: M-Shop
acknowledgement: "Open Access funding provided by IST Austria. We thank Armel Nicolas
and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante,
and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and
Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the
Miba Machine shop for their support. We also thank Wanda Kukulski (University of
Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group
for helpful discussions. Matt Swulius and Jessica Heebner provided great support
in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure
illustration.\r\n\r\nThis research was supported by the Scientific Service Units
of ISTA through resources provided by Scientific Computing, the Lab Support Facility,
and the Electron Microscopy Facility. We acknowledge funding support from the following
sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation
of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds
(to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the
European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt),
and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been
made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (to F.K.M. Schur)."
article_number: e202309125
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- 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: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- 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: Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal
the ultrastructural landscape of extracellular matrix. Journal of Cell Biology.
2024;223(6). doi:10.1083/jcb.202309125
apa: Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V.,
… Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202309125
chicago: Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler,
Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and
Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller
University Press, 2024. https://doi.org/10.1083/jcb.202309125.
ieee: B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural
landscape of extracellular matrix,” Journal of Cell Biology, vol. 223,
no. 6. Rockefeller University Press, 2024.
ista: Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V,
Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the
ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6),
e202309125.
mla: Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural
Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223,
no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.
short: B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V.
Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).
corr_author: '1'
date_created: 2024-03-21T06:45:51Z
date_published: 2024-03-20T00:00:00Z
date_updated: 2025-09-04T13:17:16Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: MiSi
- _id: Bio
- _id: EM-Fac
doi: 10.1083/jcb.202309125
ec_funded: 1
external_id:
isi:
- '001264190100001'
pmid:
- '38506714'
file:
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checksum: 90d1984a93660735e506c2a304bc3f73
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T12:52:04Z
date_updated: 2024-03-25T12:52:04Z
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file_name: 2024_JCB_Zens.pdf
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intvolume: ' 223'
isi: 1
issue: '6'
language:
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month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 7bd318a1-9f16-11ee-852c-cc9217763180
grant_number: E435
name: In Situ Actin Structures via Hybrid Cryo-electron Microscopy
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
- _id: 2615199A-B435-11E9-9278-68D0E5697425
grant_number: '21317'
name: Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ visual proteomics and structure determination
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular
matrix
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: 223
year: '2024'
...