---
_id: '14494'
abstract:
- lang: eng
text: "We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly
outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt)
for the hydrological year 2019. Information about the variables and units can
be found in the figures (.png) associated to each dataset. Details about the datasets
can be found in the original publication by Buri and others (2023).\r\n\r\nBuri,
P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ...
& Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance
of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water
Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841"
article_processing_charge: No
author:
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Simone
full_name: Fatichi, Simone
last_name: Fatichi
- first_name: Thomas
full_name: Shaw, Thomas
id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e
last_name: Shaw
orcid: 0000-0001-7640-6152
- first_name: 'Evan '
full_name: 'Miles, Evan '
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: McCarthy
- first_name: Catriona Louise
full_name: Fyffe, Catriona Louise
id: 001b0422-8d15-11ed-bc51-cab6c037a228
last_name: Fyffe
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Shaoting
full_name: Ren, Shaoting
last_name: Ren
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Jakob
full_name: Steiner, Jakob
last_name: Steiner
- first_name: Koji
full_name: Fujita, Koji
last_name: Fujita
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling
in the Himalayas: on the importance of evaporative fluxes for the water balance
of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426'
apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., …
Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas:
on the importance of evaporative fluxes for the water balance of a high elevation
catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426'
chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy,
Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface
Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water
Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426.'
ieee: 'P. Buri et al., “Model output data to ‘Land surface modeling in the
Himalayas: on the importance of evaporative fluxes for the water balance of a
high elevation catchment.’” Zenodo, 2023.'
ista: 'Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S,
Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output
data to ‘Land surface modeling in the Himalayas: on the importance of evaporative
fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.'
mla: 'Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the
Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a
High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.'
short: P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger,
S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023).
date_created: 2023-11-07T08:01:39Z
date_published: 2023-10-03T00:00:00Z
date_updated: 2025-09-09T13:15:39Z
day: '03'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.5281/ZENODO.8402426
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://10.5281/ZENODO.8402426
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14487'
relation: used_in_publication
status: public
status: public
title: 'Model output data to "Land surface modeling in the Himalayas: on the importance
of evaporative fluxes for the water balance of a high elevation catchment"'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14499'
abstract:
- lang: eng
text: "An n-vertex graph is called C-Ramsey if it has no clique or independent set
of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper,
we study edge statistics in Ramsey graphs, in particular obtaining very precise
control of the distribution of the number of edges in a random vertex subset of
a C-Ramsey graph. This brings together two ongoing lines of research: the study
of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability
for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds
via an ‘additive structure’ dichotomy on the degree sequence and involves a wide
range of different tools from Fourier analysis, random matrix theory, the theory
of Boolean functions, probabilistic combinatorics and low-rank approximation.
In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright
theorem on small-ball probability for polynomials of Gaussians, which we believe
is of independent interest. One of the consequences of our result is the resolution
of an old conjecture of Erdős and McKay, for which Erdős reiterated in several
of his open problem collections and for which he offered one of his notorious
monetary prizes."
acknowledgement: Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’
No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship
Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was
supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research
Fellowship.
article_number: e21
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Ashwin
full_name: Sah, Ashwin
last_name: Sah
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
- first_name: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
citation:
ama: Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs
and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 2023;11.
doi:10.1017/fmp.2023.17
apa: Kwan, M. A., Sah, A., Sauermann, L., & Sawhney, M. (2023). Anticoncentration
in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics,
Pi. Cambridge University Press. https://doi.org/10.1017/fmp.2023.17
chicago: Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration
in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics,
Pi. Cambridge University Press, 2023. https://doi.org/10.1017/fmp.2023.17.
ieee: M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey
graphs and a proof of the Erdős–McKay conjecture,” Forum of Mathematics, Pi,
vol. 11. Cambridge University Press, 2023.
ista: Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey
graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11,
e21.
mla: Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof
of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi, vol. 11, e21,
Cambridge University Press, 2023, doi:10.1017/fmp.2023.17.
short: M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11
(2023).
corr_author: '1'
date_created: 2023-11-07T09:02:48Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2025-09-09T13:16:15Z
day: '24'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1017/fmp.2023.17
external_id:
arxiv:
- '2208.02874'
isi:
- '001123866200001'
file:
- access_level: open_access
checksum: 54b824098d59073cc87a308d458b0a3e
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T09:16:23Z
date_updated: 2023-11-07T09:16:23Z
file_id: '14500'
file_name: 2023_ForumMathematics_Kwan.pdf
file_size: 1218719
relation: main_file
success: 1
file_date_updated: 2023-11-07T09:16:23Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Mathematical Physics
- Statistics and Probability
- Algebra and Number Theory
- Analysis
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: Forum of Mathematics, Pi
publication_identifier:
issn:
- 2050-5086
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture
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: 11
year: '2023'
...
---
_id: '14502'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized fila- mentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- 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: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023.
doi:10.15479/AT:ISTA:14502
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:14502.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data.” Institute of Science and Technology Austria, 2023.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.
mla: Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14502.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).
corr_author: '1'
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2025-04-15T08:25:41Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
file:
- access_level: open_access
checksum: a8b9adeb53a4109dea4d5e39fa1acccf
content_type: application/zip
creator: fschur
date_created: 2023-11-08T20:23:07Z
date_updated: 2023-11-08T20:23:07Z
file_id: '14503'
file_name: Computational_Toolbox_v1.2.zip
file_size: 347641117
relation: main_file
success: 1
- access_level: open_access
checksum: 14db2addbfca61a085ba301ed6f2900b
content_type: text/plain
creator: dernst
date_created: 2023-11-21T08:20:23Z
date_updated: 2023-11-21T08:20:23Z
file_id: '14586'
file_name: Readme.txt
file_size: 1522
relation: main_file
success: 1
file_date_updated: 2023-11-21T08:20:23Z
has_accepted_license: '1'
keyword:
- cryo-electron tomography
- actin cytoskeleton
- toolbox
license: https://choosealicense.com/licenses/agpl-3.0/
month: '11'
oa: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10290'
relation: used_for_analysis_in
status: public
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
tmp:
legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html
name: GNU Affero General Public License v3.0
short: 'GNU AGPLv3 '
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14513'
abstract:
- lang: eng
text: Cold atomic gases have become a paradigmatic system for exploring fundamental
physics, which at the same time allows for applications in quantum technologies.
The accelerating developments in the field have led to a highly advanced set of
engineering techniques that, for example, can tune interactions, shape the external
geometry, select among a large set of atomic species with different properties,
or control the number of atoms. In particular, it is possible to operate in lower
dimensions and drive atomic systems into the strongly correlated regime. In this
review, we discuss recent advances in few-body cold atom systems confined in low
dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in
one dimension and provide an introduction to the static properties before we review
the state-of-the-art research into quantum dynamical processes stimulated by the
presence of correlations. Besides discussing the fundamental physical phenomena
arising in these systems, we also provide an overview of the calculational and
numerical tools and methods that are commonly used, thus delivering a balanced
and comprehensive overview of the field. We conclude by giving an outlook on possible
future directions that are interesting to explore in these correlated systems.
acknowledgement: This review could not have been written without the many fruitful
discussions and great collaborations with colleagues throughout the years, there
are too many to mention. Here we acknowledge conversations regarding the context
of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro,
Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and
Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for
ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number
JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for
Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F.
and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento
Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges
support by European Union’s Horizon 2020 research and innovation programme under
the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the
Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft
(DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent
Research Fund Denmark .
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: S. I.
full_name: Mistakidis, S. I.
last_name: Mistakidis
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: R. E.
full_name: Barfknecht, R. E.
last_name: Barfknecht
- first_name: T.
full_name: Fogarty, T.
last_name: Fogarty
- first_name: Th
full_name: Busch, Th
last_name: Busch
- first_name: A.
full_name: Foerster, A.
last_name: Foerster
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
- first_name: N. T.
full_name: Zinner, N. T.
last_name: Zinner
citation:
ama: Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low
dimensions - A laboratory for quantum dynamics. Physics Reports. 2023;1042:1-108.
doi:10.1016/j.physrep.2023.10.004
apa: Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T.,
Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions -
A laboratory for quantum dynamics. Physics Reports. Elsevier. https://doi.org/10.1016/j.physrep.2023.10.004
chicago: Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch,
A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions
- A Laboratory for Quantum Dynamics.” Physics Reports. Elsevier, 2023.
https://doi.org/10.1016/j.physrep.2023.10.004.
ieee: S. I. Mistakidis et al., “Few-body Bose gases in low dimensions - A
laboratory for quantum dynamics,” Physics Reports, vol. 1042. Elsevier,
pp. 1–108, 2023.
ista: Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A,
Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory
for quantum dynamics. Physics Reports. 1042, 1–108.
mla: Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory
for Quantum Dynamics.” Physics Reports, vol. 1042, Elsevier, 2023, pp.
1–108, doi:10.1016/j.physrep.2023.10.004.
short: S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A.
Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108.
date_created: 2023-11-12T23:00:54Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2025-09-09T13:16:58Z
day: '29'
department:
- _id: MiLe
doi: 10.1016/j.physrep.2023.10.004
ec_funded: 1
external_id:
arxiv:
- '2202.11071'
isi:
- '001109871200001'
intvolume: ' 1042'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2202.11071
month: '11'
oa: 1
oa_version: Preprint
page: 1-108
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physics Reports
publication_identifier:
issn:
- 0370-1573
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Few-body Bose gases in low dimensions - A laboratory for quantum dynamics
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1042
year: '2023'
...
---
_id: '14514'
abstract:
- lang: eng
text: 'The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered
onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous
bouncing or steady-state floating. The effect embodies an unexplored interplay
between thermodynamics, elasticity, and lubrication: despite being observed, its
basic theoretical description remains a challenge. Here, we provide a theory of
elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to
the hot surface. By contrast, we discover an elasticity-dominated regime where
the heavier the solid, the higher it floats. This geometry-governed behavior is
reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this
elastic regime is characterized by Hertzian behavior of the solid’s underbelly
and derive how the float height scales with materials parameters. Introducing
a dimensionless elastic Leidenfrost number, we capture the crossover between rigid
and Hertzian behavior. Our results provide theoretical underpinning for recent
experiments, and point to the design of novel soft machines.'
acknowledgement: "We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua
Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge
the support of the Engineering and Physical Sciences Research Council (EPSRC) through
New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal
Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1,
EP/S022848/1, EP/S029966/1, and EP/P031684/1."
article_number: '168201'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta V.
full_name: Chubynsky, Mykyta V.
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James E.
full_name: Sprittles, James E.
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201
apa: Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation
of soft elastic solids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.131.168201
chicago: Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz
Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling
Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.
ieee: J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic
solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society,
2023.
ista: Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles
JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical
Review Letters. 131(16), 168201.
mla: Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.”
Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society,
2023, doi:10.1103/PhysRevLett.131.168201.
short: J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2025-09-09T13:19:07Z
day: '20'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevLett.131.168201
external_id:
isi:
- '001164388300007'
pmid:
- '37925690'
file:
- access_level: open_access
checksum: 1a419e25b762aadffbcc8eb2e609bd97
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:12:58Z
date_updated: 2023-11-13T09:12:58Z
file_id: '14524'
file_name: 2023_PhysRevLetters_Binysh.pdf
file_size: 724098
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:12:58Z
has_accepted_license: '1'
intvolume: ' 131'
isi: 1
issue: '16'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14523'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Modeling Leidenfrost levitation of soft elastic solids
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: 131
year: '2023'
...
---
_id: '14515'
abstract:
- lang: eng
text: Most natural and engineered information-processing systems transmit information
via signals that vary in time. Computing the information transmission rate or
the information encoded in the temporal characteristics of these signals requires
the mutual information between the input and output signals as a function of time,
i.e., between the input and output trajectories. Yet, this is notoriously difficult
because of the high-dimensional nature of the trajectory space, and all existing
techniques require approximations. We present an exact Monte Carlo technique called
path weight sampling (PWS) that, for the first time, makes it possible to compute
the mutual information between input and output trajectories for any stochastic
system that is described by a master equation. The principal idea is to use the
master equation to evaluate the exact conditional probability of an individual
output trajectory for a given input trajectory and average this via Monte Carlo
sampling in trajectory space to obtain the mutual information. We present three
variants of PWS, which all generate the trajectories using the standard stochastic
simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth
PWS exploits the analogy between signal trajectory sampling and polymer sampling,
and thermodynamic integration PWS is based on a reversible work calculation in
trajectory space. PWS also makes it possible to compute the mutual information
between input and output trajectories for systems with hidden internal states
as well as systems with feedback from output to input. Applying PWS to the bacterial
chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates
not only that the scheme is highly efficient but also that the number of receptor
clusters is much smaller than hitherto believed, while their size is much larger.
acknowledgement: "We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis,
and Daan Frenkel for useful discussions and a careful reading of the manuscript,
and we thank Age Tjalma for support with obtaining the Gaussian approximation of
the chemotaxis system. This work is part of the Dutch Research Council (NWO) and
was performed at the research institute AMOLF. This project has received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially
supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant
(024.003.019)."
article_number: '041017'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Manuel
full_name: Reinhardt, Manuel
last_name: Reinhardt
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein
full_name: Ten Wolde, Pieter Rein
last_name: Ten Wolde
citation:
ama: 'Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo
computation of the mutual information between stochastic trajectories. Physical
Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017'
apa: 'Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling:
Exact Monte Carlo computation of the mutual information between stochastic trajectories.
Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017'
chicago: 'Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight
Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic
Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.'
ieee: 'M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact
Monte Carlo computation of the mutual information between stochastic trajectories,”
Physical Review X, vol. 13, no. 4. American Physical Society, 2023.'
ista: 'Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte
Carlo computation of the mutual information between stochastic trajectories. Physical
Review X. 13(4), 041017.'
mla: 'Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation
of the Mutual Information between Stochastic Trajectories.” Physical Review
X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.'
short: M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-26T00:00:00Z
date_updated: 2025-09-09T13:18:24Z
day: '26'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevX.13.041017
external_id:
arxiv:
- '2203.03461'
isi:
- '001122894200001'
file:
- access_level: open_access
checksum: 32574aeebcca7347a4152c611b66b3d5
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:00:19Z
date_updated: 2023-11-13T09:00:19Z
file_id: '14522'
file_name: 2023_PhysReviewX_Reinhardt.pdf
file_size: 1595223
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:00:19Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Path weight sampling: Exact Monte Carlo computation of the mutual information
between stochastic trajectories'
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: '2023'
...
---
_id: '14516'
abstract:
- lang: eng
text: 'We revisit decentralized random beacons with a focus on practical distributed
applications. Decentralized random beacons (Beaver and So, Eurocrypt''93) provide
the functionality for n parties to generate an unpredictable sequence of bits
in a way that cannot be biased, which is useful for any decentralized protocol
requiring trusted randomness. Existing beacon constructions are highly inefficient
in practical settings where protocol parties need to rejoin after crashes or disconnections,
and more significantly where smart contracts may rely on arbitrary index points
in high-volume streams. For this, we introduce a new notion of history-generating
decentralized random beacons (HGDRBs). Roughly, the history-generation property
of HGDRBs allows for previous beacon outputs to be efficiently generated knowing
only the current value and the public key. At application layers, history-generation
supports registering a sparser set of on-chain values if desired, so that apps
like lotteries can utilize on-chain values without incurring high-frequency costs,
enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose
chains. Unlike rollups, HG is tailored specifically to recovering and verifying
pseudorandom bit sequences and thus enjoys unique optimizations investigated in
this work. We introduce STROBE: an efficient HGDRB construction which generalizes
the original squaring-based RSA approach of Beaver and So. STROBE enjoys several
useful properties that make it suited for practical applications that use beacons:
1) history-generating: it can regenerate and verify high-throughput beacon streams,
supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying:
NIZK-free, with state and validation employing a single ring element; 3) eco-friendly:
stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations
of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient:
the last beacon suffices to derive all past outputs, thus O(1) storage requirements
for nodes serving the whole history.'
acknowledgement: Work done when all the authors were at Novi Research, Meta.
alternative_title:
- LIPIcs
article_number: '7'
article_processing_charge: Yes
author:
- first_name: Donald
full_name: Beaver, Donald
last_name: Beaver
- first_name: Mahimna
full_name: Kelkar, Mahimna
last_name: Kelkar
- first_name: Kevin
full_name: Lewi, Kevin
last_name: Lewi
- first_name: Valeria
full_name: Nikolaenko, Valeria
last_name: Nikolaenko
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Konstantinos
full_name: Chalkias, Konstantinos
last_name: Chalkias
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ladi De
full_name: Naurois, Ladi De
last_name: Naurois
- first_name: Arnab
full_name: Roy, Arnab
last_name: Roy
citation:
ama: 'Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons.
In: 5th Conference on Advances in Financial Technologies. Vol 282. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.AFT.2023.7'
apa: 'Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K.,
… Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In 5th Conference
on Advances in Financial Technologies (Vol. 282). Princeton, NJ, United States:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.AFT.2023.7'
chicago: 'Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto
Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and
Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In 5th Conference
on Advances in Financial Technologies, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.AFT.2023.7.'
ieee: 'D. Beaver et al., “STROBE: Streaming Threshold Random Beacons,” in
5th Conference on Advances in Financial Technologies, Princeton, NJ, United
States, 2023, vol. 282.'
ista: 'Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris
Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons.
5th Conference on Advances in Financial Technologies. AFT: Conference on Advances
in Financial Technologies, LIPIcs, vol. 282, 7.'
mla: 'Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” 5th
Conference on Advances in Financial Technologies, vol. 282, 7, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.AFT.2023.7.'
short: D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E.
Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial
Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-10-25
location: Princeton, NJ, United States
name: 'AFT: Conference on Advances in Financial Technologies'
start_date: 2023-10-23
corr_author: '1'
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-10-09T21:07:17Z
day: '01'
ddc:
- '000'
department:
- _id: ElKo
doi: 10.4230/LIPIcs.AFT.2023.7
file:
- access_level: open_access
checksum: c1f98831cb5149d6c030c41999e6e960
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T08:44:34Z
date_updated: 2023-11-13T08:44:34Z
file_id: '14521'
file_name: 2023_LIPIcs_Beaver.pdf
file_size: 793495
relation: main_file
success: 1
file_date_updated: 2023-11-13T08:44:34Z
has_accepted_license: '1'
intvolume: ' 282'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/1643
month: '10'
oa: 1
oa_version: Published Version
publication: 5th Conference on Advances in Financial Technologies
publication_identifier:
isbn:
- '9783959773034'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'STROBE: Streaming Threshold Random Beacons'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2023'
...
---
_id: '14518'
abstract:
- lang: eng
text: We consider bidding games, a class of two-player zero-sum graph games. The
game proceeds as follows. Both players have bounded budgets. A token is placed
on a vertex of a graph, in each turn the players simultaneously submit bids, and
the higher bidder moves the token, where we break bidding ties in favor of Player
1. Player 1 wins the game iff the token visits a designated target vertex. We
consider, for the first time, poorman discrete-bidding in which the granularity
of the bids is restricted and the higher bid is paid to the bank. Previous work
either did not impose granularity restrictions or considered Richman bidding (bids
are paid to the opponent). While the latter mechanisms are technically more accessible,
the former is more appealing from a practical standpoint. Our study focuses on
threshold budgets, which is the necessary and sufficient initial budget required
for Player 1 to ensure winning against a given Player 2 budget. We first show
existence of thresholds. In DAGs, we show that threshold budgets can be approximated
with error bounds by thresholds under continuous-bidding and that they exhibit
a periodic behavior. We identify closed-form solutions in special cases. We implement
and experiment with an algorithm to find threshold budgets.
acknowledgement: This research was supported in part by ISF grant no. 1679/21, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.
article_processing_charge: No
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Suman
full_name: Sadhukhan, Suman
last_name: Sadhukhan
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman
discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications.
Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264'
apa: 'Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D.
(2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial
Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS
Press. https://doi.org/10.3233/FAIA230264'
chicago: Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde
Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial
Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264.
ieee: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability
poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and
Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148.
ista: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability
poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications.
ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.'
mla: Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers
in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp.
141–48, doi:10.3233/FAIA230264.
short: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers
in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.
conference:
end_date: 2023-10-04
location: Krakow, Poland
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2023-09-30
corr_author: '1'
date_created: 2023-11-12T23:00:56Z
date_published: 2023-09-28T00:00:00Z
date_updated: 2025-03-31T16:01:09Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.3233/FAIA230264
ec_funded: 1
external_id:
arxiv:
- '2307.15218'
file:
- access_level: open_access
checksum: 1390ca38480fa4cf286b0f1a42e8c12f
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T10:16:10Z
date_updated: 2023-11-13T10:16:10Z
file_id: '14529'
file_name: 2023_FAIA_Avni.pdf
file_size: 501011
relation: main_file
success: 1
file_date_updated: 2023-11-13T10:16:10Z
has_accepted_license: '1'
intvolume: ' 372'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 141-148
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Frontiers in Artificial Intelligence and Applications
publication_identifier:
isbn:
- '9781643684369'
issn:
- 0922-6389
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachability poorman discrete-bidding games
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 372
year: '2023'
...
---
_id: '14523'
abstract:
- lang: eng
text: see Readme file
article_processing_charge: No
author:
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Indrajit
full_name: Chakraborty, Indrajit
last_name: Chakraborty
- first_name: Mykyta
full_name: Chubynsky, Mykyta
last_name: Chubynsky
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: James
full_name: Sprittles, James
last_name: Sprittles
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
citation:
ama: 'Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. 2023. doi:10.5281/ZENODO.8329143'
apa: 'Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis,
S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143'
chicago: 'Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian,
Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.'
ieee: 'J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1.” Zenodo, 2023.'
ista: 'Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles
J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
v1.0.1, Zenodo, 10.5281/ZENODO.8329143.'
mla: 'Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids:
V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143.'
short: J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis,
J. Sprittles, A. Souslov, (2023).
date_created: 2023-11-13T09:12:11Z
date_published: 2023-09-08T00:00:00Z
date_updated: 2025-09-09T13:19:07Z
day: '08'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.5281/ZENODO.8329143
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.8329143
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14514'
relation: used_in_publication
status: public
status: public
title: 'SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14551'
abstract:
- lang: eng
text: Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome
functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How
mCG is established and transmitted across generations despite imperfect enzyme
fidelity is unclear. Whether mCG variation in natural populations is governed
by genetic or epigenetic inheritance also remains mysterious. Here, we show that
MET1 de novo activity, which is enhanced by existing proximate methylation, seeds
and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted
by active demethylation and suppressed by histone variant H2A.Z, producing localized
mCG patterns. Based on these observations, we develop a stochastic mathematical
model that precisely recapitulates mCG inheritance dynamics and predicts intragenic
mCG patterns and their population-scale variation given only CG site spacing.
Our results demonstrate that intragenic mCG establishment, inheritance, and variance
constitute a unified epigenetic process, revealing that intragenic mCG undergoes
large, millennia-long epigenetic fluctuations and can therefore mediate evolution
on this timescale.
acknowledgement: We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and
Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic
Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council
grant MaintainMeth (725746) to D.Z.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Zaigham
full_name: Shahzad, Zaigham
last_name: Shahzad
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations
generate intragenic DNA methylation variance in Arabidopsis populations. Cell
Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
apa: Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M.,
& Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic
DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2023.10.007
chicago: Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David
B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations
Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell
Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
ieee: A. Briffa et al., “Millennia-long epigenetic fluctuations generate
intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems,
vol. 14, no. 11. Elsevier, pp. 953–967, 2023.
ista: Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D.
2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.
mla: Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic
DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol.
14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.
short: A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D.
Zilberman, Cell Systems 14 (2023) 953–967.
corr_author: '1'
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2025-09-09T13:28:50Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.cels.2023.10.007
ec_funded: 1
external_id:
isi:
- '001113459100001'
pmid:
- '37944515'
file:
- access_level: open_access
checksum: 101fdac59e6f1102d68ef91f2b5bd51a
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:22:52Z
date_updated: 2023-11-20T11:22:52Z
file_id: '14580'
file_name: 2023_CellSystems_Briffa.pdf
file_size: 5587897
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:22:52Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 953-967
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations
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: 14
year: '2023'
...
---
OA_place: repository
OA_type: green
_id: '14552'
abstract:
- lang: eng
text: Interactions between plants and herbivores are central in most ecosystems,
but their strength is highly variable. The amount of variability within a system
is thought to influence most aspects of plant-herbivore biology, from ecological
stability to plant defense evolution. Our understanding of what influences variability,
however, is limited by sparse data. We collected standardized surveys of herbivory
for 503 plant species at 790 sites across 116° of latitude. With these data, we
show that within-population variability in herbivory increases with latitude,
decreases with plant size, and is phylogenetically structured. Differences in
the magnitude of variability are thus central to how plant-herbivore biology varies
across macroscale gradients. We argue that increased focus on interaction variability
will advance understanding of patterns of life on Earth.
acknowledgement: The authors acknowledge funding for central project coordination
from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution,
and Behavior Program at Michigan State University; and AgBioResearch at Michigan
State University. Site-specific funding is listed in the supplementary materials.
article_processing_charge: No
article_type: original
author:
- first_name: M. L.
full_name: Robinson, M. L.
last_name: Robinson
- first_name: P. G.
full_name: Hahn, P. G.
last_name: Hahn
- first_name: B. D.
full_name: Inouye, B. D.
last_name: Inouye
- first_name: N.
full_name: Underwood, N.
last_name: Underwood
- first_name: S. R.
full_name: Whitehead, S. R.
last_name: Whitehead
- first_name: K. C.
full_name: Abbott, K. C.
last_name: Abbott
- first_name: E. M.
full_name: Bruna, E. M.
last_name: Bruna
- first_name: N. I.
full_name: Cacho, N. I.
last_name: Cacho
- first_name: L. A.
full_name: Dyer, L. A.
last_name: Dyer
- first_name: L.
full_name: Abdala-Roberts, L.
last_name: Abdala-Roberts
- first_name: W. J.
full_name: Allen, W. J.
last_name: Allen
- first_name: J. F.
full_name: Andrade, J. F.
last_name: Andrade
- first_name: D. F.
full_name: Angulo, D. F.
last_name: Angulo
- first_name: D.
full_name: Anjos, D.
last_name: Anjos
- first_name: D. N.
full_name: Anstett, D. N.
last_name: Anstett
- first_name: R.
full_name: Bagchi, R.
last_name: Bagchi
- first_name: S.
full_name: Bagchi, S.
last_name: Bagchi
- first_name: M.
full_name: Barbosa, M.
last_name: Barbosa
- first_name: S.
full_name: Barrett, S.
last_name: Barrett
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: E.
full_name: Ben-Simchon, E.
last_name: Ben-Simchon
- first_name: K. J.
full_name: Bloodworth, K. J.
last_name: Bloodworth
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full_name: Bronstein, J. L.
last_name: Bronstein
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last_name: Buckley
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full_name: Burghardt, K. T.
last_name: Burghardt
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full_name: Bustos-Segura, C.
last_name: Bustos-Segura
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last_name: Calixto
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last_name: Sobral
- first_name: G. C.
full_name: Stotz, G. C.
last_name: Stotz
- first_name: A. J.M.
full_name: Tack, A. J.M.
last_name: Tack
- first_name: M.
full_name: Tayal, M.
last_name: Tayal
- first_name: J. F.
full_name: Tooker, J. F.
last_name: Tooker
- first_name: D.
full_name: Torrico-Bazoberry, D.
last_name: Torrico-Bazoberry
- first_name: K.
full_name: Tougeron, K.
last_name: Tougeron
- first_name: A. M.
full_name: Trowbridge, A. M.
last_name: Trowbridge
- first_name: S.
full_name: Utsumi, S.
last_name: Utsumi
- first_name: O.
full_name: Uyi, O.
last_name: Uyi
- first_name: J. L.
full_name: Vaca-Uribe, J. L.
last_name: Vaca-Uribe
- first_name: A.
full_name: Valtonen, A.
last_name: Valtonen
- first_name: L. J.A.
full_name: Van Dijk, L. J.A.
last_name: Van Dijk
- first_name: V.
full_name: Vandvik, V.
last_name: Vandvik
- first_name: J.
full_name: Villellas, J.
last_name: Villellas
- first_name: L. P.
full_name: Waller, L. P.
last_name: Waller
- first_name: M. G.
full_name: Weber, M. G.
last_name: Weber
- first_name: A.
full_name: Yamawo, A.
last_name: Yamawo
- first_name: S.
full_name: Yim, S.
last_name: Yim
- first_name: P. L.
full_name: Zarnetske, P. L.
last_name: Zarnetske
- first_name: L. N.
full_name: Zehr, L. N.
last_name: Zehr
- first_name: Z.
full_name: Zhong, Z.
last_name: Zhong
- first_name: W. C.
full_name: Wetzel, W. C.
last_name: Wetzel
citation:
ama: Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny
explain within-population variability in herbivory. Science. 2023;382(6671):679-683.
doi:10.1126/science.adh8830
apa: Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R.,
Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain
within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830
chicago: Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead,
K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain
within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.
ieee: M. L. Robinson et al., “Plant size, latitude, and phylogeny explain
within-population variability in herbivory,” Science, vol. 382, no. 6671.
AAAS, pp. 679–683, 2023.
ista: Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population
variability in herbivory. Science. 382(6671), 679–683.
mla: Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population
Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp.
679–83, doi:10.1126/science.adh8830.
short: M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C.
Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F.
Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa,
S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M.
Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol,
M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen,
D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco,
H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D.
Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes,
M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M.
França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M.
Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L.
Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm,
M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban,
R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu,
J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López,
M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M.
Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia,
R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C.
Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R.
Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor,
H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q.
Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal,
F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann,
C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M.
Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant,
H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P.
Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker,
D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe,
A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber,
A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382
(2023) 679–683.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-09T00:00:00Z
date_updated: 2025-09-09T13:23:56Z
day: '09'
department:
- _id: NiBa
doi: 10.1126/science.adh8830
external_id:
isi:
- '001138596500033'
pmid:
- '37943897'
intvolume: ' 382'
isi: 1
issue: '6671'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://centaur.reading.ac.uk/113962/1/adh8830_CombinedPDF_v6.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 679-683
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '14579'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Plant size, latitude, and phylogeny explain within-population variability in
herbivory
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 382
year: '2023'
...
---
_id: '14553'
abstract:
- lang: eng
text: Quantum state tomography is an essential component of modern quantum technology.
In application to continuous-variable harmonic-oscillator systems, such as the
electromagnetic field, existing tomography methods typically reconstruct the state
in discrete bases, and are hence limited to states with relatively low amplitudes
and energies. Here, we overcome this limitation by utilizing a feed-forward neural
network to obtain the density matrix directly in the continuous position basis.
An important benefit of our approach is the ability to choose specific regions
in the phase space for detailed reconstruction. This results in a relatively slow
scaling of the amount of resources required for the reconstruction with the state
amplitude, and hence allows us to dramatically increase the range of amplitudes
accessible with our method.
article_number: '042430'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ekaterina
full_name: Fedotova, Ekaterina
id: c1bea5e1-878e-11ee-9dff-d7404e4422ab
last_name: Fedotova
orcid: 0000-0001-7242-015X
- first_name: Nikolai
full_name: Kuznetsov, Nikolai
last_name: Kuznetsov
- first_name: Egor
full_name: Tiunov, Egor
last_name: Tiunov
- first_name: A. E.
full_name: Ulanov, A. E.
last_name: Ulanov
- first_name: A. I.
full_name: Lvovsky, A. I.
last_name: Lvovsky
citation:
ama: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 2023;108(4).
doi:10.1103/PhysRevA.108.042430
apa: Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I.
(2023). Continuous-variable quantum tomography of high-amplitude states. Physical
Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430
chicago: Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and
A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.”
Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430.
ieee: E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable
quantum tomography of high-amplitude states,” Physical Review A, vol. 108,
no. 4. American Physical Society, 2023.
ista: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable
quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.
mla: Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude
States.” Physical Review A, vol. 108, no. 4, 042430, American Physical
Society, 2023, doi:10.1103/PhysRevA.108.042430.
short: E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical
Review A 108 (2023).
corr_author: '1'
date_created: 2023-11-19T23:00:54Z
date_published: 2023-10-30T00:00:00Z
date_updated: 2024-10-09T21:07:19Z
day: '30'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.108.042430
external_id:
arxiv:
- '2212.07406'
intvolume: ' 108'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.07406
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous-variable quantum tomography of high-amplitude states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14554'
abstract:
- lang: eng
text: 'The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors
and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations
around the meanfield limit for large-scale particle systems in both particle density
and momentum density. We focus on the following two aspects. Firstly, we set up
a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide
suitable definitions of numerical fluxes at the interface of the mesh elements
which are consistent with the wave-type nature of the RIDK model and grant stability
of the simulations, and we quantify the rate of convergence in mean square to
the continuous RIDK model. Secondly, we introduce modifications of the RIDK model
in order to preserve positivity of the density (such a feature only holds in a
“high-probability sense” for the original RIDK model). By means of numerical simulations,
we show that the modifications lead to physically realistic and positive density
profiles. In one case, subject to additional regularity constraints, we also prove
positivity. Finally, we present an application of our methodology to a system
of diffusing and reacting particles. Our Python code is available in open-source
format.'
acknowledgement: "The authors thank the anonymous referees for their careful reading
of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges
funding from the Austrian Science Fund (FWF) through the project F65, and from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered
the first part of this project)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
citation:
ama: 'Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077'
apa: 'Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki
equation: Discontinuous Galerkin approximation and modelling for low-density regime.
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077'
chicago: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’
Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density
Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences,
2023. https://doi.org/10.1051/m2an/2023077.'
ieee: 'F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM:
Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences,
pp. 3061–3090, 2023.'
ista: 'Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation:
Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM:
Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.'
mla: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki
Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.”
ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP
Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.'
short: 'F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis
57 (2023) 3061–3090.'
corr_author: '1'
date_created: 2023-11-19T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-09-09T13:21:05Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1051/m2an/2023077
ec_funded: 1
external_id:
isi:
- '001087237700001'
file:
- access_level: open_access
checksum: 3aef1475b1882c8dec112df9a5167c39
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:34:57Z
date_updated: 2023-11-20T08:34:57Z
file_id: '14560'
file_name: 2023_ESAIM_Cornalba.pdf
file_size: 1508534
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:34:57Z
has_accepted_license: '1'
intvolume: ' 57'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 3061-3090
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'ESAIM: Mathematical Modelling and Numerical Analysis'
publication_identifier:
eissn:
- 2804-7214
issn:
- 2822-7840
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/tonyshardlow/RIDK-FD
scopus_import: '1'
status: public
title: 'The regularised inertial Dean'' Kawasaki equation: Discontinuous Galerkin
approximation and modelling for low-density regime'
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: 57
year: '2023'
...
---
_id: '14555'
abstract:
- lang: eng
text: The intricate regulatory processes behind actin polymerization play a crucial
role in cellular biology, including essential mechanisms such as cell migration
or cell division. However, the self-organizing principles governing actin polymerization
are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky
(BZ) reaction, a classic and well understood chemical oscillator known for its
self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing
actin. While the BZ reaction originates from the domain of inorganic chemistry,
it shares remarkable similarities with actin polymerization, including the characteristic
propagating waves, which are influenced by geometry and external fields, and the
emergent collective behavior. Starting with a general description of emerging
patterns, we elaborate on single droplets or cell-level dynamics, the influence
of geometric confinements and conclude with collective interactions. Comparing
these two systems sheds light on the universal nature of self-organization principles
in both living and inanimate systems.
acknowledgement: The author(s) declare that no financial support was received for
the research, authorship, and/or publication of this article.
article_number: '1287420'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky
reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420
apa: Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin
and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental
Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420
chicago: Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.
ieee: M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology,
vol. 11. Frontiers, 2023.
ista: Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the
Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11,
1287420.
mla: Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing
Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental
Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420.
short: M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).
corr_author: '1'
date_created: 2023-11-19T23:00:55Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2025-09-09T13:22:00Z
day: '31'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3389/fcell.2023.1287420
external_id:
isi:
- '001100762800001'
pmid:
- '38020899'
file:
- access_level: open_access
checksum: 61857fc3ebf019354932e7ee684658ce
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T08:41:15Z
date_updated: 2023-11-20T08:41:15Z
file_id: '14561'
file_name: 2023_FrontiersCellDevBio_Riedl.pdf
file_size: 2047622
relation: main_file
success: 1
file_date_updated: 2023-11-20T08:41:15Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction
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: 11
year: '2023'
...
---
_id: '14556'
abstract:
- lang: eng
text: Inversions are structural mutations that reverse the sequence of a chromosome
segment and reduce the effective rate of recombination in the heterozygous state.
They play a major role in adaptation, as well as in other evolutionary processes
such as speciation. Although inversions have been studied since the 1920s, they
remain difficult to investigate because the reduced recombination conferred by
them strengthens the effects of drift and hitchhiking, which in turn can obscure
signatures of selection. Nonetheless, numerous inversions have been found to be
under selection. Given recent advances in population genetic theory and empirical
study, here we review how different mechanisms of selection affect the evolution
of inversions. A key difference between inversions and other mutations, such as
single nucleotide variants, is that the fitness of an inversion may be affected
by a larger number of frequently interacting processes. This considerably complicates
the analysis of the causes underlying the evolution of inversions. We discuss
the extent to which these mechanisms can be disentangled, and by which approach.
acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments
on a previous version of our manuscript. This paper was conceived at the ESEB Progress
Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’,
organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between
28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop
and to the following funding bodies for supporting our research: ERC AdG 101055327
to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141
to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND
and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência
e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss
National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science
Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation
(SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian
Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262
and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane
Zinn (Flatt lab) for help with reference formatting.'
article_number: '14242'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
- first_name: Kimberly J.
full_name: Gilbert, Kimberly J.
last_name: Gilbert
- first_name: Paul
full_name: Jay, Paul
last_name: Jay
- first_name: Martin
full_name: Kapun, Martin
last_name: Kapun
- first_name: Katie E.
full_name: Lotterhos, Katie E.
last_name: Lotterhos
- first_name: Claire
full_name: Mérot, Claire
last_name: Mérot
- first_name: Esra
full_name: Durmaz Mitchell, Esra
last_name: Durmaz Mitchell
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
- first_name: Catherine L.
full_name: Peichel, Catherine L.
last_name: Peichel
- 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: Stephen W.
full_name: Schaeffer, Stephen W.
last_name: Schaeffer
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Thomas
full_name: Flatt, Thomas
last_name: Flatt
citation:
ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient
the evolutionary process. Journal of Evolutionary Biology. 2023;36(12).
doi:10.1111/jeb.14242
apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata,
I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process.
Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242
chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui
Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient
the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023.
https://doi.org/10.1111/jeb.14242.
ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary
process,” Journal of Evolutionary Biology, vol. 36, no. 12. Wiley, 2023.
ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert
KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel
CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How
chromosomal inversions reorient the evolutionary process. Journal of Evolutionary
Biology. 36(12), 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, vol. 36, no. 12, 14242, Wiley,
2023, doi:10.1111/jeb.14242.
short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata,
K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell,
M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson,
T. Flatt, Journal of Evolutionary Biology 36 (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2025-09-09T13:22:35Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
external_id:
isi:
- '001098690500001'
pmid:
- '37942504'
file:
- access_level: open_access
checksum: 93ae4fa700aab8646bc62f0adeed8f8f
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T08:16:31Z
date_updated: 2024-07-16T08:16:31Z
file_id: '17253'
file_name: 2023_JourEvolutionaryBio_Berdan.pdf
file_size: 1401726
relation: main_file
success: 1
file_date_updated: 2024-07-16T08:16:31Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: How chromosomal inversions reorient the evolutionary process
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2023'
...
---
_id: '14557'
abstract:
- lang: eng
text: Motivated by a problem posed in [10], we investigate the closure operators
of the category SLatt of join semilattices and its subcategory SLattO of join
semilattices with bottom element. In particular, we show that there are only finitely
many closure operators of both categories, and provide a complete classification.
We use this result to deduce the known fact that epimorphisms of SLatt and SLattO
are surjective. We complement the paper with two different proofs of this result
using either generators or Isbell’s zigzag theorem.
acknowledgement: "The first and second named authors are members of GNSAGA – INdAM.\r\nThe
third named author was supported by the FWF Grant, Project number I4245–N35"
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Dikranjan, D.
last_name: Dikranjan
- first_name: A.
full_name: Giordano Bruno, A.
last_name: Giordano Bruno
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
citation:
ama: Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of
categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221.
doi:10.2989/16073606.2023.2247731
apa: Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and
closure operators of categories of semilattices. Quaestiones Mathematicae.
Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731
chicago: Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure
Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor
& Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731.
ieee: D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators
of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no.
S1. Taylor & Francis, pp. 191–221, 2023.
ista: Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators
of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221.
mla: Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of
Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor &
Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.
short: D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023)
191–221.
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2025-09-09T13:23:12Z
day: '01'
department:
- _id: HeEd
doi: 10.2989/16073606.2023.2247731
external_id:
isi:
- '001098712000006'
intvolume: ' 46'
isi: 1
issue: S1
language:
- iso: eng
month: '11'
oa_version: None
page: 191-221
project:
- _id: 26AD5D90-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04245
name: Algebraic Footprints of Geometric Features in Homology
publication: Quaestiones Mathematicae
publication_identifier:
eissn:
- 1727-933X
issn:
- 1607-3606
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Epimorphisms and closure operators of categories of semilattices
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2023'
...
---
_id: '14558'
abstract:
- lang: eng
text: "n the dynamic minimum set cover problem, the challenge is to minimize the
update time while guaranteeing a close-to-optimal min{O(log n), f} approximation
factor. (Throughout, n, m, f , and C are parameters denoting the maximum number
of elements, the number of sets, the frequency, and the cost range.) In the high-frequency
range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation
algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic
algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this
paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic
algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on
the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work,
the best approximation ratio guaranteed by deterministic algorithms was O(f2)
of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual
method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only
result with O(f) -approximation was that of Abboud et al. [Dynamic set cover:
Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125],
who designed a randomized (1+∈)f -approximation algorithm with amortized update
time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the
above update time bound for most values of f\r\n in the low-frequency range, i.e.,
f=o(log n) . It is also the first result that is independent of m\r\n and n. It
subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically
maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update
time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex
cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time:
No nontrivial worst-case update time was previously known for the dynamic set
cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly
(∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem
(i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully
dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst
case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our
results via the primal-dual approach, by maintaining a fractional packing solution
as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual
approach uses a local update scheme that maintains relaxed complementary slackness
conditions for every set. For our first result we use instead a global update
scheme that does not always maintain complementary slackness conditions. For our
second result we combine the global and the local update schema. To achieve our
third result we use a hierarchy of background schedulers. It is an interesting
open question whether this background scheduler technique can also be used to
transform algorithms with amortized running time bounds into algorithms with worst-case
running time bounds."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council,
UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the
Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer
(ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung,
2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I
5982-N, and project Z 422-N. The third author was also supported by the Swedish
Research Council (Reg. No. 2015-04659). The fourth author was also supported by
the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ,
0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023)."
article_processing_charge: No
article_type: original
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- 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: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
- first_name: Xiaowei
full_name: Wu, Xiaowei
last_name: Wu
citation:
ama: Bhattacharya S, Henzinger M, Nanongkai D, Wu X. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing.
2023;52(5):1132-1192. doi:10.1137/21M1428649
apa: Bhattacharya, S., Henzinger, M., Nanongkai, D., & Wu, X. (2023). Deterministic
near-optimal approximation algorithms for dynamic set cover. SIAM Journal on
Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649
chicago: Bhattacharya, Sayan, Monika Henzinger, Danupon Nanongkai, and Xiaowei Wu.
“Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM
Journal on Computing. Society for Industrial and Applied Mathematics, 2023.
https://doi.org/10.1137/21M1428649.
ieee: S. Bhattacharya, M. Henzinger, D. Nanongkai, and X. Wu, “Deterministic near-optimal
approximation algorithms for dynamic set cover,” SIAM Journal on Computing,
vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192,
2023.
ista: Bhattacharya S, Henzinger M, Nanongkai D, Wu X. 2023. Deterministic near-optimal
approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5),
1132–1192.
mla: Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms
for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society
for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649.
short: S. Bhattacharya, M. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing
52 (2023) 1132–1192.
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-09-09T13:19:49Z
day: '01'
department:
- _id: MoHe
doi: 10.1137/21M1428649
ec_funded: 1
external_id:
isi:
- '001116719500002'
intvolume: ' 52'
isi: 1
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 1132-1192
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deterministic near-optimal approximation algorithms for dynamic set cover
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 52
year: '2023'
...
---
_id: '14559'
abstract:
- lang: eng
text: We consider the problem of learning control policies in discrete-time stochastic
systems which guarantee that the system stabilizes within some specified stabilization
region with probability 1. Our approach is based on the novel notion of stabilizing
ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome
the limitation of methods proposed in previous works whose applicability is restricted
to systems in which the stabilizing region cannot be left once entered under any
control policy. We present a learning procedure that learns a control policy together
with an sRSM that formally certifies probability 1 stability, both learned as
neural networks. We show that this procedure can also be adapted to formally verifying
that, under a given Lipschitz continuous control policy, the stochastic system
stabilizes within some stabilizing region with probability 1. Our experimental
evaluation shows that our learning procedure can successfully learn provably stabilizing
policies in practice.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Matin
full_name: Ansaripour, Matin
last_name: Ansaripour
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably
stabilizing neural controllers for discrete-time stochastic systems. In: 21st
International Symposium on Automated Technology for Verification and Analysis.
Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17'
apa: 'Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic,
D. (2023). Learning provably stabilizing neural controllers for discrete-time
stochastic systems. In 21st International Symposium on Automated Technology
for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore:
Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17'
chicago: Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner,
and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time
Stochastic Systems.” In 21st International Symposium on Automated Technology
for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17.
ieee: M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic,
“Learning provably stabilizing neural controllers for discrete-time stochastic
systems,” in 21st International Symposium on Automated Technology for Verification
and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.
ista: 'Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning
provably stabilizing neural controllers for discrete-time stochastic systems.
21st International Symposium on Automated Technology for Verification and Analysis.
ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.'
mla: Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers
for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated
Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023,
pp. 357–79, doi:10.1007/978-3-031-45329-8_17.
short: M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:,
21st International Symposium on Automated Technology for Verification and Analysis,
Springer Nature, 2023, pp. 357–379.
conference:
end_date: 2023-10-27
location: Singapore, Singapore
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2023-10-24
corr_author: '1'
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-22T00:00:00Z
date_updated: 2025-09-09T13:20:26Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-031-45329-8_17
ec_funded: 1
external_id:
arxiv:
- '2210.05304'
isi:
- '001456127300017'
intvolume: ' 14215'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2210.05304'
month: '10'
oa: 1
oa_version: Preprint
page: 357-379
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 21st International Symposium on Automated Technology for Verification
and Analysis
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031453281'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning provably stabilizing neural controllers for discrete-time stochastic
systems
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14215
year: '2023'
...
---
_id: '14562'
abstract:
- lang: eng
text: "Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nFunding: This research was supported by the Scientific Service
Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the
Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the
Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group
GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft
(DFG) to J.F. and K.R."
article_processing_charge: No
author:
- 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: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.” 2023.
doi:10.15479/AT:ISTA:14562
apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562
chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.
ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.’” Institute
of Science and Technology Austria, 2023.
ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.
mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.
short: F.K. Schur, (2023).
contributor:
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- contributor_type: researcher
first_name: Georgi A
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last_name: Dimchev
orcid: 0000-0001-8370-6161
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last_name: Hodirnau
- contributor_type: researcher
first_name: Jan
last_name: Faix
- contributor_type: researcher
first_name: Klemens
last_name: Rottner
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
corr_author: '1'
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2025-04-23T08:46:21Z
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project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
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status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
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legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
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BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
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...
---
_id: '14564'
abstract:
- lang: eng
text: Cumulus parameterization (CP) in state‐of‐the‐art global climate models is
based on the quasi‐equilibrium assumption (QEA), which views convection as the
action of an ensemble of cumulus clouds, in a state of equilibrium with respect
to a slowly varying atmospheric state. This view is not compatible with the organization
and dynamical interactions across multiple scales of cloud systems in the tropics
and progress in this research area was slow over decades despite the widely recognized
major shortcomings. Novel ideas on how to represent key physical processes of
moist convection‐large‐scale interaction to overcome the QEA have surged recently.
The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions
of multiple cloud types that characterize organized tropical convection. Here,
the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in
which the bulk mass flux and bulk entrainment and detrainment rates are calculated.
This is done by introducing a stochastic ensemble of plumes characterized by randomly
varying detrainment level distributions based on the cloud area fraction of the
SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in
a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated
against the control ZM scheme in the context of the single column Community Climate
Model of the National Center for Atmospheric Research using data from both tropical
ocean and midlatitude land convection. Some key features of the SMCM CP such as
it capability to represent the tri‐modal nature of organized convection are emphasized.
acknowledgement: The research of B.K. is supported in part by a Discovery Grant from
the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020).
This research was conducted during the visits of P.M. Krishna to the Center for
Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November
2018 to June 2019 and July 2019 and October 2019, respectively. The authors are
very grateful to the three anonymous reviewers who provided very thoughtful and
constructive comments during the review process that helped greatly improve and
shape the final version of the manuscript.
article_number: e2022MS003391
article_processing_charge: Yes
article_type: original
author:
- first_name: B.
full_name: Khouider, B.
last_name: Khouider
- first_name: BIDYUT B
full_name: GOSWAMI, BIDYUT B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: GOSWAMI
orcid: 0000-0001-8602-3083
- first_name: R.
full_name: Phani, R.
last_name: Phani
- first_name: A. J.
full_name: Majda, A. J.
last_name: Majda
citation:
ama: Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391
apa: Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep
unified stochastic mass flux cumulus parameterization in the single column community
climate model. Journal of Advances in Modeling Earth Systems. American
Geophysical Union. https://doi.org/10.1029/2022ms003391
chicago: Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep
Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community
Climate Model.” Journal of Advances in Modeling Earth Systems. American
Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391.
ieee: B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified
stochastic mass flux cumulus parameterization in the single column community climate
model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11.
American Geophysical Union, 2023.
ista: Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic
mass flux cumulus parameterization in the single column community climate model.
Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.
mla: Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization
in the Single Column Community Climate Model.” Journal of Advances in Modeling
Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union,
2023, doi:10.1029/2022ms003391.
short: B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling
Earth Systems 15 (2023).
date_created: 2023-11-20T09:18:21Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2025-09-09T13:29:45Z
day: '01'
ddc:
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department:
- _id: CaMu
doi: 10.1029/2022ms003391
external_id:
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has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '11'
keyword:
- General Earth and Planetary Sciences
- Environmental Chemistry
- Global and Planetary Change
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: A shallow‐deep unified stochastic mass flux cumulus parameterization in the
single column community climate model
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2023'
...