---
_id: '13221'
abstract:
- lang: eng
text: The safety-liveness dichotomy is a fundamental concept in formal languages
which plays a key role in verification. Recently, this dichotomy has been lifted
to quantitative properties, which are arbitrary functions from infinite words
to partially-ordered domains. We look into harnessing the dichotomy for the specific
classes of quantitative properties expressed by quantitative automata. These automata
contain finitely many states and rational-valued transition weights, and their
common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum
map infinite words into the totallyordered domain of real numbers. In this automata-theoretic
setting, we establish a connection between quantitative safety and topological
continuity and provide an alternative characterization of quantitative safety
and liveness in terms of their boolean counterparts. For all common value functions,
we show how the safety closure of a quantitative automaton can be constructed
in PTime, and we provide PSpace-complete checks of whether a given quantitative
automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata,
for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf,
and LimSup automata, we give PTime decompositions into safe and live automata.
These decompositions enable the separation of techniques for safety and liveness
verification for quantitative specifications.
acknowledgement: We thank Christof Löding for pointing us to some results on PSpace-hardess
of universality problems and the anonymous reviewers for their helpful comments.
This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science
Foundation grant 2410/22.
alternative_title:
- LIPIcs
article_number: '17'
article_processing_charge: No
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- 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: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative
automata. In: 34th International Conference on Concurrency Theory. Vol
279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17'
apa: 'Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023).
Safety and liveness of quantitative automata. In 34th International Conference
on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17'
chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac.
“Safety and Liveness of Quantitative Automata.” In 34th International Conference
on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.
ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness
of quantitative automata,” in 34th International Conference on Concurrency
Theory, Antwerp, Belgium, 2023, vol. 279.
ista: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness
of quantitative automata. 34th International Conference on Concurrency Theory.
CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.'
mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th
International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17.
short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-09-23
location: Antwerp, Belgium
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2023-09-18
date_created: 2023-07-14T10:00:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-10-09T07:14:03Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2023.17
ec_funded: 1
external_id:
arxiv:
- '2307.06016'
file:
- access_level: open_access
checksum: d40e57a04448ea5c77d7e1cfb9590a81
content_type: application/pdf
creator: esarac
date_created: 2023-07-14T12:03:48Z
date_updated: 2023-07-14T12:03:48Z
file_id: '13224'
file_name: CONCUR23.pdf
file_size: 755529
relation: main_file
success: 1
file_date_updated: 2023-07-14T12:03:48Z
has_accepted_license: '1'
intvolume: ' 279'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 34th International Conference on Concurrency Theory
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772990'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: Safety and liveness of quantitative automata
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: 279
year: '2023'
...
---
_id: '14406'
abstract:
- lang: eng
text: "Recently, a concept of generalized multifractality, which characterizes fluctuations
and correlations of critical eigenstates, was introduced and explored for all
10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model
(\r\nNL\r\nσ\r\nM\r\n) field theory, we extend the theory of generalized multifractality
to boundaries of systems at criticality. Our numerical simulations on two-dimensional
systems of symmetry classes A, C, and AII fully confirm the analytical predictions
of pure-scaling observables and Weyl symmetry relations between critical exponents
of surface generalized multifractality. This demonstrates the validity of the
\r\nNL\r\nσ\r\nM\r\n for the description of Anderson-localization critical phenomena,
not only in the bulk but also on the boundary. The critical exponents strongly
violate generalized parabolicity, in analogy with earlier results for the bulk,
corroborating the conclusion that the considered Anderson-localization critical
points are not described by conformal field theories. We further derive relations
between generalized surface multifractal spectra and linear combinations of Lyapunov
exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption
of invariance with respect to a logarithmic conformal map. Our numerics demonstrate
that these relations hold with an excellent accuracy. Taken together, our results
indicate an intriguing situation: the conformal invariance is broken but holds
partially at critical points of Anderson localization."
acknowledgement: "We thank Ilya Gruzberg for many illuminating discussions. S.S.B.,
J.F.K., and A.D.M. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG)
via the Grant\r\nNo. MI 658/14-1. I.S.B. acknowledges support from Russian Science
Foundation (Grant No. 22-42-04416)."
article_number: '104205'
article_processing_charge: No
article_type: original
author:
- first_name: Serafim
full_name: Babkin, Serafim
id: 41e64307-6672-11ee-b9ad-cc7a0075a479
last_name: Babkin
orcid: 0009-0003-7382-8036
- first_name: Jonas F.
full_name: Karcher, Jonas F.
last_name: Karcher
- first_name: Igor S.
full_name: Burmistrov, Igor S.
last_name: Burmistrov
- first_name: Alexander D.
full_name: Mirlin, Alexander D.
last_name: Mirlin
citation:
ama: Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. Generalized surface multifractality
in two-dimensional disordered systems. Physical Review B. 2023;108(10).
doi:10.1103/PhysRevB.108.104205
apa: Babkin, S., Karcher, J. F., Burmistrov, I. S., & Mirlin, A. D. (2023).
Generalized surface multifractality in two-dimensional disordered systems. Physical
Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.104205
chicago: Babkin, Serafim, Jonas F. Karcher, Igor S. Burmistrov, and Alexander D.
Mirlin. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.104205.
ieee: S. Babkin, J. F. Karcher, I. S. Burmistrov, and A. D. Mirlin, “Generalized
surface multifractality in two-dimensional disordered systems,” Physical Review
B, vol. 108, no. 10. American Physical Society, 2023.
ista: Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. 2023. Generalized surface
multifractality in two-dimensional disordered systems. Physical Review B. 108(10),
104205.
mla: Babkin, Serafim, et al. “Generalized Surface Multifractality in Two-Dimensional
Disordered Systems.” Physical Review B, vol. 108, no. 10, 104205, American
Physical Society, 2023, doi:10.1103/PhysRevB.108.104205.
short: S. Babkin, J.F. Karcher, I.S. Burmistrov, A.D. Mirlin, Physical Review B
108 (2023).
date_created: 2023-10-08T22:01:17Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-10-09T07:09:30Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.108.104205
external_id:
arxiv:
- '2306.09455'
intvolume: ' 108'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.09455
month: '09'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalized surface multifractality in two-dimensional disordered systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14410'
abstract:
- lang: eng
text: This paper focuses on the implementation details of the baseline methods and
a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming
data under class-prior shift. LIMES achieves superior performance over the baseline
methods, especially concerning the minimum-across-day accuracy, which is important
for the users of the system. In this work, the key measures to facilitate reproducibility
and enhance the credibility of the results are described.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Paulina
full_name: Tomaszewska, Paulina
last_name: Tomaszewska
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Tomaszewska P, Lampert C. On the implementation of baselines and lightweight
conditional model extrapolation (LIMES) under class-prior shift. In: International
Workshop on Reproducible Research in Pattern Recognition. Vol 14068. Springer
Nature; 2023:67-73. doi:10.1007/978-3-031-40773-4_6'
apa: 'Tomaszewska, P., & Lampert, C. (2023). On the implementation of baselines
and lightweight conditional model extrapolation (LIMES) under class-prior shift.
In International Workshop on Reproducible Research in Pattern Recognition
(Vol. 14068, pp. 67–73). Montreal, Canada: Springer Nature. https://doi.org/10.1007/978-3-031-40773-4_6'
chicago: Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines
and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.”
In International Workshop on Reproducible Research in Pattern Recognition,
14068:67–73. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-40773-4_6.
ieee: P. Tomaszewska and C. Lampert, “On the implementation of baselines and lightweight
conditional model extrapolation (LIMES) under class-prior shift,” in International
Workshop on Reproducible Research in Pattern Recognition, Montreal, Canada,
2023, vol. 14068, pp. 67–73.
ista: 'Tomaszewska P, Lampert C. 2023. On the implementation of baselines and lightweight
conditional model extrapolation (LIMES) under class-prior shift. International
Workshop on Reproducible Research in Pattern Recognition. RRPR: Reproducible Research
in Pattern Recognition, LNCS, vol. 14068, 67–73.'
mla: Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines
and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.”
International Workshop on Reproducible Research in Pattern Recognition,
vol. 14068, Springer Nature, 2023, pp. 67–73, doi:10.1007/978-3-031-40773-4_6.
short: P. Tomaszewska, C. Lampert, in:, International Workshop on Reproducible Research
in Pattern Recognition, Springer Nature, 2023, pp. 67–73.
conference:
end_date: 2022-08-21
location: Montreal, Canada
name: 'RRPR: Reproducible Research in Pattern Recognition'
start_date: 2022-08-21
date_created: 2023-10-08T22:01:18Z
date_published: 2023-08-20T00:00:00Z
date_updated: 2023-10-09T06:48:02Z
day: '20'
department:
- _id: ChLa
doi: 10.1007/978-3-031-40773-4_6
intvolume: ' 14068'
language:
- iso: eng
month: '08'
oa_version: None
page: 67-73
publication: International Workshop on Reproducible Research in Pattern Recognition
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031407727'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the implementation of baselines and lightweight conditional model extrapolation
(LIMES) under class-prior shift
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14068
year: '2023'
...
---
_id: '14405'
abstract:
- lang: eng
text: We introduce hypernode automata as a new specification formalism for hyperproperties
of concurrent systems. They are finite automata with nodes labeled with hypernode
logic formulas and transitions labeled with actions. A hypernode logic formula
specifies relations between sequences of variable values in different system executions.
Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces
by constraining the values and the order of value changes of each variable without
correlating the timing of the changes. Different execution traces are synchronized
solely through the transitions of hypernode automata. Hypernode automata naturally
combine asynchronicity at the node level with synchronicity at the transition
level. We show that the model-checking problem for hypernode automata is decidable
over action-labeled Kripke structures, whose actions induce transitions of the
specification automata. For this reason, hypernode automaton is a suitable formalism
for specifying and verifying asynchronous hyperproperties, such as declassifying
observational determinism in multi-threaded programs.
acknowledgement: "This work was supported in part by the Austrian Science Fund (FWF)
SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the
ERC Advanced Grant\r\nVAMOS 101020093."
alternative_title:
- LIPIcs
article_number: '21'
article_processing_charge: Yes
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- 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: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana
full_name: Oliveira da Costa, Ana
id: f347ec37-6676-11ee-b395-a888cb7b4fb4
last_name: Oliveira da Costa
orcid: 0000-0002-8741-5799
citation:
ama: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata.
In: 34th International Conference on Concurrency Theory. Vol 279. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.21'
apa: 'Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A.
(2023). Hypernode automata. In 34th International Conference on Concurrency
Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.21'
chicago: Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da
Costa. “Hypernode Automata.” In 34th International Conference on Concurrency
Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
https://doi.org/10.4230/LIPIcs.CONCUR.2023.21.
ieee: E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode
automata,” in 34th International Conference on Concurrency Theory, Antwerp,
Belgium, 2023, vol. 279.
ista: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode
automata. 34th International Conference on Concurrency Theory. CONCUR: Conference
on Concurrency Theory, LIPIcs, vol. 279, 21.'
mla: Bartocci, Ezio, et al. “Hypernode Automata.” 34th International Conference
on Concurrency Theory, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.21.
short: E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th
International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023.
conference:
end_date: 2023-09-22
location: Antwerp, Belgium
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2023-09-19
date_created: 2023-10-08T22:01:16Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-10-09T07:43:44Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2023.21
ec_funded: 1
external_id:
arxiv:
- '2305.02836'
file:
- access_level: open_access
checksum: 215765e40454d806174ac0a223e8d6fa
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T07:42:45Z
date_updated: 2023-10-09T07:42:45Z
file_id: '14413'
file_name: 2023_LIPcs_Bartocci.pdf
file_size: 795790
relation: main_file
success: 1
file_date_updated: 2023-10-09T07:42:45Z
has_accepted_license: '1'
intvolume: ' 279'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 34th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959772990'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hypernode automata
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: 279
year: '2023'
...
---
_id: '14408'
abstract:
- lang: eng
text: "We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues
{σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries
are asymptotically Gaussian for any H20-functions f around any point z0 in the
bulk of the spectrum on any mesoscopic scale 0Probability Theory and Related Fields. 2023. doi:10.1007/s00440-023-01229-1
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Mesoscopic central
limit theorem for non-Hermitian random matrices. Probability Theory and Related
Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01229-1
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Mesoscopic Central
Limit Theorem for Non-Hermitian Random Matrices.” Probability Theory and Related
Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-023-01229-1.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Mesoscopic central limit theorem
for non-Hermitian random matrices,” Probability Theory and Related Fields.
Springer Nature, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Mesoscopic central limit theorem
for non-Hermitian random matrices. Probability Theory and Related Fields.
mla: Cipolloni, Giorgio, et al. “Mesoscopic Central Limit Theorem for Non-Hermitian
Random Matrices.” Probability Theory and Related Fields, Springer Nature,
2023, doi:10.1007/s00440-023-01229-1.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields
(2023).
date_created: 2023-10-08T22:01:17Z
date_published: 2023-09-28T00:00:00Z
date_updated: 2023-10-09T07:19:01Z
day: '28'
department:
- _id: LaEr
doi: 10.1007/s00440-023-01229-1
external_id:
arxiv:
- '2210.12060'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.12060
month: '09'
oa: 1
oa_version: Preprint
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- 1432-2064
issn:
- 0178-8051
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mesoscopic central limit theorem for non-Hermitian random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14404'
abstract:
- lang: eng
text: A light-triggered fabrication method extends the functionality of printable
nanomaterials
acknowledgement: The authors thank the Werner-Siemens-Stiftung and the Institute of
Science and Technology Austria for financial support.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Balazs D, Ibáñez M. Widening the use of 3D printing. Science. 2023;381(6665):1413-1414.
doi:10.1126/science.adk3070
apa: Balazs, D., & Ibáñez, M. (2023). Widening the use of 3D printing. Science.
AAAS. https://doi.org/10.1126/science.adk3070
chicago: Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science.
AAAS, 2023. https://doi.org/10.1126/science.adk3070.
ieee: D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” Science,
vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.
ista: Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665),
1413–1414.
mla: Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” Science,
vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:10.1126/science.adk3070.
short: D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.
date_created: 2023-10-08T22:01:16Z
date_published: 2023-09-29T00:00:00Z
date_updated: 2023-10-09T07:32:58Z
day: '29'
department:
- _id: MaIb
- _id: LifeSc
doi: 10.1126/science.adk3070
external_id:
pmid:
- '37769110'
intvolume: ' 381'
issue: '6665'
language:
- iso: eng
month: '09'
oa_version: None
page: 1413-1414
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Widening the use of 3D printing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '14417'
abstract:
- lang: eng
text: Entropic risk (ERisk) is an established risk measure in finance, quantifying
risk by an exponential re-weighting of rewards. We study ERisk for the first time
in the context of turn-based stochastic games with the total reward objective.
This gives rise to an objective function that demands the control of systems in
a risk-averse manner. We show that the resulting games are determined and, in
particular, admit optimal memoryless deterministic strategies. This contrasts
risk measures that previously have been considered in the special case of Markov
decision processes and that require randomization and/or memory. We provide several
results on the decidability and the computational complexity of the threshold
problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In
the most general case, the problem is decidable subject to Shanuel’s conjecture.
If all inputs are rational, the resulting threshold problem can be solved using
algebraic numbers, leading to decidability via a polynomial-time reduction to
the existential theory of the reals. Further restrictions on the encoding of the
input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation
algorithm for the optimal value of ERisk is provided.
acknowledgement: "This work was partly funded by the ERC CoG 863818 (ForM-SMArt),
the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software
Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as
part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1."
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: Yes
author:
- first_name: Christel
full_name: Baier, Christel
last_name: Baier
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Jakob
full_name: Piribauer, Jakob
last_name: Piribauer
citation:
ama: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based
stochastic games. In: 48th International Symposium on Mathematical Foundations
of Computer Science. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.MFCS.2023.15'
apa: 'Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2023). Entropic
risk for turn-based stochastic games. In 48th International Symposium on Mathematical
Foundations of Computer Science (Vol. 272). Bordeaux, France: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2023.15'
chicago: Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob
Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In 48th International
Symposium on Mathematical Foundations of Computer Science, Vol. 272. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.MFCS.2023.15.
ieee: C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk
for turn-based stochastic games,” in 48th International Symposium on Mathematical
Foundations of Computer Science, Bordeaux, France, 2023, vol. 272.
ista: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for
turn-based stochastic games. 48th International Symposium on Mathematical Foundations
of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science,
LIPIcs, vol. 272, 15.'
mla: Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” 48th
International Symposium on Mathematical Foundations of Computer Science, vol.
272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.MFCS.2023.15.
short: C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International
Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-09-01
location: Bordeaux, France
name: 'MFCS: Symposium on Mathematical Foundations of Computer Science'
start_date: 2023-08-28
date_created: 2023-10-09T09:21:05Z
date_published: 2023-08-21T00:00:00Z
date_updated: 2023-10-09T09:22:37Z
day: '21'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2023.15
ec_funded: 1
external_id:
arxiv:
- '2307.06611'
file:
- access_level: open_access
checksum: 402281b17ed669bbf149d0fdf68ac201
content_type: application/pdf
creator: dernst
date_created: 2023-10-09T09:19:11Z
date_updated: 2023-10-09T09:19:11Z
file_id: '14418'
file_name: 2023_LIPIcsMFCS_Baier.pdf
file_size: 826843
relation: main_file
success: 1
file_date_updated: 2023-10-09T09:19:11Z
has_accepted_license: '1'
intvolume: ' 272'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 48th International Symposium on Mathematical Foundations of Computer
Science
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772921'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Entropic risk for turn-based stochastic games
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: 272
year: '2023'
...
---
_id: '12960'
abstract:
- lang: eng
text: "Isomanifolds are the generalization of isosurfaces to arbitrary dimension
and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate
multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the
manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider
its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the
ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds
from a given starting point. The algorithm works for arbitrary dimensions n and
d, and any precision D. Our main result is that, when f (or M) has bounded complexity,
the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably
exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and
isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds
of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality
reduction techniques, the dependency on d in the size of M^ can be completely
removed with high probability. We also show that the algorithm can handle isomanifolds
with boundary and, more generally, isostratifolds. The algorithm for isomanifolds
with boundary has been implemented and experimental results are reported, showing
that it is practical and can handle cases that are far ahead of the state-of-the-art. "
acknowledgement: The authors have received funding from the European Research Council
under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations
of Geometric Un-derstanding in Higher Dimensions). The first author was supported by the French government,through
the 3IA C\^ote d'Azur Investments in the Future project managed by the National
ResearchAgency (ANR) with the reference ANR-19-P3IA-0002. The third author was
supported by the Eu-ropean Union's Horizon 2020 research and innovation programme
under the Marie Sk\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science
Fund) grant M 3073.
article_processing_charge: No
article_type: original
author:
- first_name: Jean Daniel
full_name: Boissonnat, Jean Daniel
last_name: Boissonnat
- first_name: Siargey
full_name: Kachanovich, Siargey
last_name: Kachanovich
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in
time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal
on Computing. 2023;52(2):452-486. doi:10.1137/21M1412918
apa: Boissonnat, J. D., Kachanovich, S., & Wintraecken, M. (2023). Tracing isomanifolds
in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM
Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1412918
chicago: Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken.
“Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn
Triangulations.” SIAM Journal on Computing. Society for Industrial and
Applied Mathematics, 2023. https://doi.org/10.1137/21M1412918.
ieee: J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds
in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,”
SIAM Journal on Computing, vol. 52, no. 2. Society for Industrial and Applied
Mathematics, pp. 452–486, 2023.
ista: Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in
Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM
Journal on Computing. 52(2), 452–486.
mla: Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial
in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing,
vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86,
doi:10.1137/21M1412918.
short: J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing
52 (2023) 452–486.
date_created: 2023-05-14T22:01:00Z
date_published: 2023-04-30T00:00:00Z
date_updated: 2023-10-10T07:34:35Z
day: '30'
department:
- _id: HeEd
doi: 10.1137/21M1412918
ec_funded: 1
external_id:
isi:
- '001013183000012'
intvolume: ' 52'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1
month: '04'
oa: 1
oa_version: Submitted Version
page: 452-486
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
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'
related_material:
record:
- id: '9441'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn
triangulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2023'
...
---
_id: '13134'
abstract:
- lang: eng
text: We propose a characterization of discrete analytical spheres, planes and lines
in the body-centered cubic (BCC) grid, both in the Cartesian and in the recently
proposed alternative compact coordinate system, in which each integer triplet
addresses some voxel in the grid. We define spheres and planes through double
Diophantine inequalities and investigate their relevant topological features,
such as functionality or the interrelation between the thickness of the objects
and their connectivity and separation properties. We define lines as the intersection
of planes. The number of the planes (up to six) is equal to the number of the
pairs of faces of a BCC voxel that are parallel to the line.
acknowledgement: The first author has been partially supported by the Ministry of
Science, Technological Development and Innovation of the Republic of Serbia through
the project no. 451-03-47/2023-01/200156. The fourth author is funded by the DFG
Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’,
Austrian Science Fund (FWF), grant no. I 02979-N35.
article_number: '109693'
article_processing_charge: No
article_type: original
author:
- first_name: Lidija
full_name: Čomić, Lidija
last_name: Čomić
- first_name: Gaëlle
full_name: Largeteau-Skapin, Gaëlle
last_name: Largeteau-Skapin
- first_name: Rita
full_name: Zrour, Rita
last_name: Zrour
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
citation:
ama: Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. Discrete analytical
objects in the body-centered cubic grid. Pattern Recognition. 2023;142(10).
doi:10.1016/j.patcog.2023.109693
apa: Čomić, L., Largeteau-Skapin, G., Zrour, R., Biswas, R., & Andres, E. (2023).
Discrete analytical objects in the body-centered cubic grid. Pattern Recognition.
Elsevier. https://doi.org/10.1016/j.patcog.2023.109693
chicago: Čomić, Lidija, Gaëlle Largeteau-Skapin, Rita Zrour, Ranita Biswas, and
Eric Andres. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” Pattern
Recognition. Elsevier, 2023. https://doi.org/10.1016/j.patcog.2023.109693.
ieee: L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, and E. Andres, “Discrete
analytical objects in the body-centered cubic grid,” Pattern Recognition,
vol. 142, no. 10. Elsevier, 2023.
ista: Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. 2023. Discrete analytical
objects in the body-centered cubic grid. Pattern Recognition. 142(10), 109693.
mla: Čomić, Lidija, et al. “Discrete Analytical Objects in the Body-Centered Cubic
Grid.” Pattern Recognition, vol. 142, no. 10, 109693, Elsevier, 2023, doi:10.1016/j.patcog.2023.109693.
short: L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, E. Andres, Pattern Recognition
142 (2023).
date_created: 2023-06-18T22:00:45Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-10T07:37:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.patcog.2023.109693
external_id:
isi:
- '001013526000001'
intvolume: ' 142'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
publication: Pattern Recognition
publication_identifier:
issn:
- 0031-3203
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discrete analytical objects in the body-centered cubic grid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2023'
...
---
_id: '13216'
abstract:
- lang: eng
text: Physical catalysts often have multiple sites where reactions can take place.
One prominent example is single-atom alloys, where the reactive dopant atoms can
preferentially locate in the bulk or at different sites on the surface of the
nanoparticle. However, ab initio modeling of catalysts usually only considers
one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles
of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation
of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using
machine learning potentials trained on density functional theory calculations,
and then the occupation of different single-atom active sites is identified using
a similarity kernel. Further, the turnover frequency for all possible sites is
calculated for propane dehydrogenation to propene through microkinetic modeling
using density functional theory calculations. The total turnover frequencies of
the whole nanoparticle are then described from both the population and the individual
turnover frequency of each site. Under operating conditions, rhodium as a dopant
is found to almost exclusively occupy (111) surface sites while palladium as a
dopant occupies a greater variety of facets. Undercoordinated dopant surface sites
are found to tend to be more reactive for propane dehydrogenation compared to
the (111) surface. It is found that considering the dynamics of the single-atom
alloy nanoparticle has a profound effect on the calculated catalytic activity
of single-atom alloys by several orders of magnitude.
acknowledgement: "B.C. acknowledges resources provided by the Cambridge Tier2 system
operated by the University of Cambridge Research\r\nComputing Service funded by
EPSRC Tier-2 capital grant EP/\r\nP020259/1."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: Felix
full_name: Wodaczek, Felix
id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e
last_name: Wodaczek
orcid: 0009-0000-1457-795X
- first_name: Tina
full_name: Torabi, Tina
last_name: Torabi
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: 'Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy
nanoparticles: Modeling the dehydrogenation of propane. Journal of the American
Chemical Society. 2023;145(27):14894-14902. doi:10.1021/jacs.3c04030'
apa: 'Bunting, R., Wodaczek, F., Torabi, T., & Cheng, B. (2023). Reactivity
of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c04030'
chicago: 'Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity
of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.”
Journal of the American Chemical Society. American Chemical Society, 2023.
https://doi.org/10.1021/jacs.3c04030.'
ieee: 'R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom
alloy nanoparticles: Modeling the dehydrogenation of propane,” Journal of the
American Chemical Society, vol. 145, no. 27. American Chemical Society, pp.
14894–14902, 2023.'
ista: 'Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom
alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American
Chemical Society. 145(27), 14894–14902.'
mla: 'Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling
the Dehydrogenation of Propane.” Journal of the American Chemical Society,
vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:10.1021/jacs.3c04030.'
short: R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical
Society 145 (2023) 14894–14902.
date_created: 2023-07-12T09:16:40Z
date_published: 2023-06-30T00:00:00Z
date_updated: 2023-10-11T08:45:10Z
day: '30'
ddc:
- '540'
department:
- _id: MaIb
- _id: BiCh
doi: 10.1021/jacs.3c04030
external_id:
isi:
- '001020623900001'
pmid:
- '37390457'
file:
- access_level: open_access
checksum: e07d5323f9c0e5cbd1ad6453f29440ab
content_type: application/pdf
creator: cchlebak
date_created: 2023-07-12T10:22:04Z
date_updated: 2023-07-12T10:22:04Z
file_id: '13219'
file_name: 2023_JACS_Bunting.pdf
file_size: 3155843
relation: main_file
success: 1
file_date_updated: 2023-07-12T10:22:04Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '27'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 14894-14902
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation
of propane'
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 145
year: '2023'
...
---
_id: '14426'
abstract:
- lang: eng
text: To meet the physiological demands of the body, organs need to establish a
functional tissue architecture and adequate size as the embryo develops to adulthood.
In the liver, uni- and bipotent progenitor differentiation into hepatocytes and
biliary epithelial cells (BECs), and their relative proportions, comprise the
functional architecture. Yet, the contribution of individual liver progenitors
at the organ level to both fates, and their specific proportion, is unresolved.
Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage
tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is
established (i) fast, (ii) solely by heterogeneous lineage decisions from uni-
and bipotent progenitors, and (iii) independent of subsequent cell type–specific
proliferation. Extending lineage tracing to adulthood determined that embryonic
cells undergo spatially heterogeneous three-dimensional growth associated with
distinct environments. Strikingly, giant clusters comprising almost half a ventral
lobe suggest lobe-specific dominant-like growth behaviours. We show substantial
hepatocyte polyploidy in juveniles representing another hallmark of postembryonic
liver growth. Our findings uncover heterogeneous progenitor contributions to tissue
architecture-defining cell type proportions and postembryonic organ growth as
key mechanisms forming the adult liver.
acknowledgement: "We thank the Ober group for discussion and comments on the manuscript.
We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T.
Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine
(AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem
Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this
work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852
(EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation
grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch
Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation
(PRL) and European Research Council (ERC) under the EU Horizon 2020 research and
Innovation Programme Grant Agreement No. 851288 (EH)."
article_number: e3002315
article_processing_charge: No
article_type: original
author:
- first_name: Iris A.
full_name: Unterweger, Iris A.
last_name: Unterweger
- first_name: Julie
full_name: Klepstad, Julie
last_name: Klepstad
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Pia R.
full_name: Lundegaard, Pia R.
last_name: Lundegaard
- first_name: Ala
full_name: Trusina, Ala
last_name: Trusina
- first_name: Elke A.
full_name: Ober, Elke A.
last_name: Ober
citation:
ama: Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage
tracing identifies heterogeneous hepatoblast contribution to cell lineages and
postembryonic organ growth dynamics. PLoS Biology. 2023;21(10). doi:10.1371/journal.pbio.3002315
apa: Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina,
A., & Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast
contribution to cell lineages and postembryonic organ growth dynamics. PLoS
Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002315
chicago: Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard,
Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast
Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS
Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002315.
ieee: I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina,
and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution
to cell lineages and postembryonic organ growth dynamics,” PLoS Biology,
vol. 21, no. 10. Public Library of Science, 2023.
ista: Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA.
2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell
lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315.
mla: Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast
Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS
Biology, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:10.1371/journal.pbio.3002315.
short: I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina,
E.A. Ober, PLoS Biology 21 (2023).
date_created: 2023-10-15T22:01:10Z
date_published: 2023-10-04T00:00:00Z
date_updated: 2023-10-16T07:25:48Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1371/journal.pbio.3002315
ec_funded: 1
file:
- access_level: open_access
checksum: 40a2b11b41d70a0e5939f8a52b66e389
content_type: application/pdf
creator: dernst
date_created: 2023-10-16T07:20:49Z
date_updated: 2023-10-16T07:20:49Z
file_id: '14431'
file_name: 2023_PloSBiology_Unterweger.pdf
file_size: 6193110
relation: main_file
success: 1
file_date_updated: 2023-10-16T07:20:49Z
has_accepted_license: '1'
intvolume: ' 21'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/JulieKlepstad/LiverDevelopment
scopus_import: '1'
status: public
title: Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages
and postembryonic organ growth dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2023'
...
---
_id: '14428'
abstract:
- lang: eng
text: "Suppose we have two hash functions h1 and h2, but we trust the security of
only one of them. To mitigate this worry, we wish to build a hash combiner Ch1,h2
which is secure so long as one of the underlying hash functions is. This question
has been well-studied in the regime of collision resistance. In this case, concatenating
the two hash function outputs clearly works. Unfortunately, a long series of works
(Boneh and Boyen, CRYPTO’06; Pietrzak, Eurocrypt’07; Pietrzak, CRYPTO’08) showed
no (noticeably) shorter combiner for collision resistance is possible.\r\nIn this
work, we revisit this pessimistic state of affairs, motivated by the observation
that collision-resistance is insufficient for many interesting applications of
cryptographic hash functions anyway. We argue the right formulation of the “hash
combiner” is to build what we call random oracle (RO) combiners, utilizing stronger
assumptions for stronger constructions.\r\nIndeed, we circumvent the previous
lower bounds for collision resistance by constructing a simple length-preserving
RO combiner C˜h1,h2Z1,Z2(M)=h1(M,Z1)⊕h2(M,Z2),where Z1,Z2\r\n are random salts
of appropriate length. We show that this extra randomness is necessary for RO
combiners, and indeed our construction is somewhat tight with this lower bound.\r\nOn
the negative side, we show that one cannot generically apply the composition theorem
to further replace “monolithic” hash functions h1 and h2 by some simpler indifferentiable
construction (such as the Merkle-Damgård transformation) from smaller components,
such as fixed-length compression functions. Finally, despite this issue, we directly
prove collision resistance of the Merkle-Damgård variant of our combiner, where
h1 and h2 are replaced by iterative Merkle-Damgård hashes applied to a fixed-length
compression function. Thus, we can still subvert the concatenation barrier for
collision-resistance combiners while utilizing practically small fixed-length
components underneath."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Niels
full_name: Ferguson, Niels
last_name: Ferguson
- first_name: Eli
full_name: Goldin, Eli
last_name: Goldin
- first_name: Peter
full_name: Hall, Peter
last_name: Hall
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. Random oracle combiners:
Breaking the concatenation barrier for collision-resistance. In: 43rd Annual
International Cryptology Conference. Vol 14082. Springer Nature; 2023:514-546.
doi:10.1007/978-3-031-38545-2_17'
apa: 'Dodis, Y., Ferguson, N., Goldin, E., Hall, P., & Pietrzak, K. Z. (2023).
Random oracle combiners: Breaking the concatenation barrier for collision-resistance.
In 43rd Annual International Cryptology Conference (Vol. 14082, pp. 514–546).
Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-38545-2_17'
chicago: 'Dodis, Yevgeniy, Niels Ferguson, Eli Goldin, Peter Hall, and Krzysztof
Z Pietrzak. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.”
In 43rd Annual International Cryptology Conference, 14082:514–46. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-38545-2_17.'
ieee: 'Y. Dodis, N. Ferguson, E. Goldin, P. Hall, and K. Z. Pietrzak, “Random oracle
combiners: Breaking the concatenation barrier for collision-resistance,” in 43rd
Annual International Cryptology Conference, Santa Barbara, CA, United States,
2023, vol. 14082, pp. 514–546.'
ista: 'Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. 2023. Random oracle combiners:
Breaking the concatenation barrier for collision-resistance. 43rd Annual International
Cryptology Conference. CRYPTO: Advances in Cryptology, LNCS, vol. 14082, 514–546.'
mla: 'Dodis, Yevgeniy, et al. “Random Oracle Combiners: Breaking the Concatenation
Barrier for Collision-Resistance.” 43rd Annual International Cryptology Conference,
vol. 14082, Springer Nature, 2023, pp. 514–46, doi:10.1007/978-3-031-38545-2_17.'
short: Y. Dodis, N. Ferguson, E. Goldin, P. Hall, K.Z. Pietrzak, in:, 43rd Annual
International Cryptology Conference, Springer Nature, 2023, pp. 514–546.
conference:
end_date: 2023-08-24
location: Santa Barbara, CA, United States
name: 'CRYPTO: Advances in Cryptology'
start_date: 2023-08-20
date_created: 2023-10-15T22:01:11Z
date_published: 2023-08-09T00:00:00Z
date_updated: 2023-10-16T08:02:11Z
day: '09'
department:
- _id: KrPi
doi: 10.1007/978-3-031-38545-2_17
intvolume: ' 14082'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/1041
month: '08'
oa: 1
oa_version: Preprint
page: 514-546
publication: 43rd Annual International Cryptology Conference
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031385445'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Random oracle combiners: Breaking the concatenation barrier for collision-resistance'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14082
year: '2023'
...
---
_id: '13052'
abstract:
- lang: eng
text: Imaging of the immunological synapse (IS) between dendritic cells (DCs) and
T cells in suspension is hampered by suboptimal alignment of cell-cell contacts
along the vertical imaging plane. This requires optical sectioning that often
results in unsatisfactory resolution in time and space. Here, we present a workflow
where DCs and T cells are confined between a layer of glass and polydimethylsiloxane
(PDMS) that orients the cells along one, horizontal imaging plane, allowing for
fast en-face-imaging of the DC-T cell IS.
acknowledged_ssus:
- _id: Bio
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'A.L. was funded by an Erwin Schrödinger postdoctoral fellowship
of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary
postdoctoral fellow. This work was supported by a European Research Council grant
ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication
facility, and the Miba Machine Shop of ISTA for their excellent support.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- 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: 'Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB.
New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9'
apa: 'Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of
T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.),
The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature.
https://doi.org/10.1007/978-1-0716-3135-5_9'
chicago: 'Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging
of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse,
edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY:
Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9.'
ieee: 'A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari
and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.'
ista: 'Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology,
vol. 2654, 137–147.'
mla: Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin,
vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.
short: A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The
Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.
date_created: 2023-05-22T08:41:48Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-10-17T08:44:53Z
day: '28'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1007/978-1-0716-3135-5_9
ec_funded: 1
editor:
- first_name: Cosima
full_name: Baldari, Cosima
last_name: Baldari
- first_name: Michael
full_name: Dustin, Michael
last_name: Dustin
external_id:
pmid:
- '37106180'
intvolume: ' 2654'
language:
- iso: eng
month: '04'
oa_version: None
page: 137-147
place: New York, NY
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: The Immune Synapse
publication_identifier:
eisbn:
- '9781071631355'
eissn:
- 1940-6029
isbn:
- '9781071631348'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2654
year: '2023'
...
---
_id: '12406'
abstract:
- lang: eng
text: Let X be a sufficiently large positive integer. We prove that one may choose
a subset S of primes with cardinality O(logX) such that a positive proportion
of integers less than X can be represented by x2+py2 for at least one p∈S.
acknowledgement: "This article is a version the author’s master thesis at the University
of Bonn. The author would like to thank his advisor Valentin Blomer for introducing
the problem, and giving generous feedback and encouragement along the way, especially
during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on
analytic number theory. Finally, the author is grateful to the anonymous referees
for their valuable time and comments.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Yijie
full_name: Diao, Yijie
id: 7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b
last_name: Diao
orcid: 0000-0002-4989-5330
citation:
ama: Diao Y. Density of the union of positive diagonal binary quadratic forms. Acta
Arithmetica. 2023;207:1-17. doi:10.4064/aa210830-24-11
apa: Diao, Y. (2023). Density of the union of positive diagonal binary quadratic
forms. Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa210830-24-11
chicago: Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic
Forms.” Acta Arithmetica. Instytut Matematyczny, 2023. https://doi.org/10.4064/aa210830-24-11.
ieee: Y. Diao, “Density of the union of positive diagonal binary quadratic forms,”
Acta Arithmetica, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.
ista: Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms.
Acta Arithmetica. 207, 1–17.
mla: Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.”
Acta Arithmetica, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:10.4064/aa210830-24-11.
short: Y. Diao, Acta Arithmetica 207 (2023) 1–17.
date_created: 2023-01-26T21:17:04Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-10-17T09:15:17Z
day: '09'
department:
- _id: GradSch
doi: 10.4064/aa210830-24-11
external_id:
arxiv:
- '2103.08268'
isi:
- '000912903000001'
intvolume: ' 207'
isi: 1
keyword:
- Algebra
- Number Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.08268
month: '01'
oa: 1
oa_version: Preprint
page: 1-17
publication: Acta Arithmetica
publication_identifier:
eissn:
- 1730-6264
issn:
- 0065-1036
publication_status: published
publisher: Instytut Matematyczny
quality_controlled: '1'
status: public
title: Density of the union of positive diagonal binary quadratic forms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 207
year: '2023'
...
---
_id: '13200'
abstract:
- lang: eng
text: Recent quantum technologies have established precise quantum control of various
microscopic systems using electromagnetic waves. Interfaces based on cryogenic
cavity electro-optic systems are particularly promising, due to the direct interaction
between microwave and optical fields in the quantum regime. Quantum optical control
of superconducting microwave circuits has been precluded so far due to the weak
electro-optical coupling as well as quasi-particles induced by the pump laser.
Here we report the coherent control of a superconducting microwave cavity using
laser pulses in a multimode electro-optical device at millikelvin temperature
with near-unity cooperativity. Both the stationary and instantaneous responses
of the microwave and optical modes comply with the coherent electro-optical interaction,
and reveal only minuscule amount of excess back-action with an unanticipated time
delay. Our demonstration enables wide ranges of applications beyond quantum transductions,
from squeezing and quantum non-demolition measurements of microwave fields, to
entanglement generation and hybrid quantum networks.
acknowledgement: This work was supported by the European Research Council under grant
agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research
and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and
the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous
support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral
fellowship with funding from the European Union’s Horizon 2020 research and innovation
program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the
recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.
article_number: '3784'
article_processing_charge: No
article_type: original
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a
superconducting microwave cavity via electro-optical dynamical back-action. Nature
Communications. 2023;14. doi:10.1038/s41467-023-39493-3
apa: Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent
optical control of a superconducting microwave cavity via electro-optical dynamical
back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3
chicago: Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M
Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical
Dynamical Back-Action.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3.
ieee: L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical
control of a superconducting microwave cavity via electro-optical dynamical back-action,”
Nature Communications, vol. 14. Nature Research, 2023.
ista: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control
of a superconducting microwave cavity via electro-optical dynamical back-action.
Nature Communications. 14, 3784.
mla: Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity
via Electro-Optical Dynamical Back-Action.” Nature Communications, vol.
14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3.
short: L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications
14 (2023).
date_created: 2023-07-09T22:01:11Z
date_published: 2023-06-24T00:00:00Z
date_updated: 2023-10-17T11:46:12Z
day: '24'
ddc:
- '000'
department:
- _id: JoFi
doi: 10.1038/s41467-023-39493-3
ec_funded: 1
external_id:
arxiv:
- '2210.12443'
isi:
- '001018100800002'
pmid:
- '37355691'
file:
- access_level: open_access
checksum: ec7ccd2c08f90d59cab302fd0d7776a4
content_type: application/pdf
creator: alisjak
date_created: 2023-07-10T10:10:54Z
date_updated: 2023-07-10T10:10:54Z
file_id: '13206'
file_name: 2023_NatureComms_Qiu.pdf
file_size: 1349134
relation: main_file
success: 1
file_date_updated: 2023-07-10T10:10:54Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coherent optical control of a superconducting microwave cavity via electro-optical
dynamical back-action
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13315'
abstract:
- lang: eng
text: How do statistical dependencies in measurement noise influence high-dimensional
inference? To answer this, we study the paradigmatic spiked matrix model of principal
components analysis (PCA), where a rank-one matrix is corrupted by additive noise.
We go beyond the usual independence assumption on the noise entries, by drawing
the noise from a low-order polynomial orthogonal matrix ensemble. The resulting
noise correlations make the setting relevant for applications but analytically
challenging. We provide characterization of the Bayes optimal limits of inference
in this model. If the spike is rotation invariant, we show that standard spectral
PCA is optimal. However, for more general priors, both PCA and the existing approximate
message-passing algorithm (AMP) fall short of achieving the information-theoretic
limits, which we compute using the replica method from statistical physics. We
thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer
equations, which is empirically observed to saturate the conjectured theoretical
limit. This AMP comes with a rigorous state evolution analysis tracking its performance.
Although we focus on specific noise distributions, our methodology can be generalized
to a wide class of trace matrix ensembles at the cost of more involved expressions.
Finally, despite the seemingly strong assumption of rotation-invariant noise,
our theory empirically predicts algorithmic performance on real data, pointing
at strong universality properties.
acknowledgement: J.B. was funded by the European Union (ERC, CHORAL, project number
101039794). Views and opinions expressed are however those of the author(s) only
and do not necessarily reflect those of the European Union or the European Research
Council. Neither the European Union nor the granting authority can be held responsible
for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank
the reviewers for the insightful comments and, in particular, for suggesting the
BAMP-inspired denoisers leading to AMP-AP.
article_number: e2302028120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jean
full_name: Barbier, Jean
last_name: Barbier
- first_name: Francesco
full_name: Camilli, Francesco
last_name: Camilli
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Manuel
full_name: Sáenz, Manuel
last_name: Sáenz
citation:
ama: Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured
principal component analysis and how to reach them. Proceedings of the National
Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120
apa: Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental
limits in structured principal component analysis and how to reach them. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2302028120
chicago: Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental
Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120.
ieee: J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in
structured principal component analysis and how to reach them,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 30. National Academy of Sciences, 2023.
ista: Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured
principal component analysis and how to reach them. Proceedings of the National
Academy of Sciences of the United States of America. 120(30), e2302028120.
mla: Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component
Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 120, no. 30, e2302028120, National Academy
of Sciences, 2023, doi:10.1073/pnas.2302028120.
short: J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National
Academy of Sciences of the United States of America 120 (2023).
date_created: 2023-07-30T22:01:02Z
date_published: 2023-07-25T00:00:00Z
date_updated: 2023-10-17T11:44:55Z
day: '25'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.1073/pnas.2302028120
external_id:
pmid:
- '37463204'
file:
- access_level: open_access
checksum: 1fc06228afdb3aa80cf8e7766bcf9dc5
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:30:48Z
date_updated: 2023-07-31T07:30:48Z
file_id: '13323'
file_name: 2023_PNAS_Barbier.pdf
file_size: 995933
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:30:48Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '30'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/fcamilli95/Structured-PCA-
scopus_import: '1'
status: public
title: Fundamental limits in structured principal component analysis and how to reach
them
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2023'
...
---
_id: '14037'
abstract:
- lang: eng
text: 'Traditionally, nuclear spin is not considered to affect biological processes.
Recently, this has changed as isotopic fractionation that deviates from classical
mass dependence was reported both in vitro and in vivo. In these cases, the isotopic
effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects
using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial
dioxygen production system and biological aquaporin channels in cells. We observe
that oxygen dynamics in chiral environments (in particular its transport) depend
on nuclear spin, suggesting future applications for controlled isotope separation
to be used, for instance, in NMR. To demonstrate the mechanism behind our findings,
we formulate theoretical models based on a nuclear-spin-enhanced switch between
electronic spin states. Accounting for the role of nuclear spin in biology can
provide insights into the role of quantum effects in living systems and help inspire
the development of future biotechnology solutions.'
acknowledgement: N.M.-S. acknowledges the support of the Ministry of Energy, Israel,
as part of the scholarship program for graduate students in the fields of energy.
M.L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation,
Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support
of the BSF-NSF 094 Grant No. 2022503.
article_number: e2300828120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ofek
full_name: Vardi, Ofek
last_name: Vardi
- first_name: Naama
full_name: Maroudas-Sklare, Naama
last_name: Maroudas-Sklare
- first_name: Yuval
full_name: Kolodny, Yuval
last_name: Kolodny
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Amijai
full_name: Saragovi, Amijai
last_name: Saragovi
- first_name: Nir
full_name: Galili, Nir
last_name: Galili
- first_name: Stav
full_name: Ferrera, Stav
last_name: Ferrera
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Nir
full_name: Yuran, Nir
last_name: Yuran
- first_name: Hagit P.
full_name: Affek, Hagit P.
last_name: Affek
- first_name: Boaz
full_name: Luz, Boaz
last_name: Luz
- first_name: Yonaton
full_name: Goldsmith, Yonaton
last_name: Goldsmith
- first_name: Nir
full_name: Keren, Nir
last_name: Keren
- first_name: Shira
full_name: Yochelis, Shira
last_name: Yochelis
- first_name: Itay
full_name: Halevy, Itay
last_name: Halevy
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
citation:
ama: Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological
processes. Proceedings of the National Academy of Sciences of the United States
of America. 2023;120(32). doi:10.1073/pnas.2300828120
apa: Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili,
N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2300828120
chicago: Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai
Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological
Processes.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.
ieee: O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32. National Academy of Sciences, 2023.
ista: Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N,
Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis
S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes.
Proceedings of the National Academy of Sciences of the United States of America.
120(32), e2300828120.
mla: Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.
short: O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili,
S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren,
S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy
of Sciences of the United States of America 120 (2023).
date_created: 2023-08-13T22:01:12Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2023-10-17T11:45:25Z
day: '31'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2300828120
ec_funded: 1
external_id:
pmid:
- '37523549'
file:
- access_level: open_access
checksum: a5ed64788a5acef9b9a300a26fa5a177
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:43:45Z
date_updated: 2023-08-14T07:43:45Z
file_id: '14047'
file_name: 2023_PNAS_Vardi.pdf
file_size: 1003092
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:43:45Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear spin effects in biological processes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2023'
...
---
_id: '12683'
abstract:
- lang: eng
text: We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗
for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In
particular, we establish that with high probability, an outlier can be distinguished
at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines
elements of Hermitian and non-Hermitian analysis, and illustrates some aspects
of the intrinsic instability of (even weakly) non-Hermitian matrices.
acknowledgement: G. Dubach gratefully acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond”
No. 101020331.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Dubach, Guillaume
id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E
last_name: Dubach
orcid: 0000-0001-6892-8137
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix.
Electronic Communications in Probability. 2023;28:1-13. doi:10.1214/23-ECP516
apa: Dubach, G., & Erdös, L. (2023). Dynamics of a rank-one perturbation of
a Hermitian matrix. Electronic Communications in Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/23-ECP516
chicago: Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation
of a Hermitian Matrix.” Electronic Communications in Probability. Institute
of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP516.
ieee: G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian
matrix,” Electronic Communications in Probability, vol. 28. Institute of
Mathematical Statistics, pp. 1–13, 2023.
ista: Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian
matrix. Electronic Communications in Probability. 28, 1–13.
mla: Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of
a Hermitian Matrix.” Electronic Communications in Probability, vol. 28,
Institute of Mathematical Statistics, 2023, pp. 1–13, doi:10.1214/23-ECP516.
short: G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.
date_created: 2023-02-26T23:01:01Z
date_published: 2023-02-08T00:00:00Z
date_updated: 2023-10-17T12:48:10Z
day: '08'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/23-ECP516
ec_funded: 1
external_id:
arxiv:
- '2108.13694'
isi:
- '000950650200005'
file:
- access_level: open_access
checksum: a1c6f0a3e33688fd71309c86a9aad86e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T09:43:27Z
date_updated: 2023-02-27T09:43:27Z
file_id: '12692'
file_name: 2023_ElectCommProbability_Dubach.pdf
file_size: 479105
relation: main_file
success: 1
file_date_updated: 2023-02-27T09:43:27Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1-13
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Electronic Communications in Probability
publication_identifier:
eissn:
- 1083-589X
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of a rank-one perturbation of a Hermitian matrix
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2023'
...
---
_id: '12761'
abstract:
- lang: eng
text: "We consider the fluctuations of regular functions f of a Wigner matrix W
viewed as an entire matrix f (W). Going beyond the well-studied tracial mode,
Trf (W), which is equivalent to the customary linear statistics of eigenvalues,
we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic
matrix A. We identify three different and asymptotically independent modes of
this fluctuation, corresponding to the tracial part, the traceless diagonal part
and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find
that the off-diagonal modes fluctuate on a much smaller scale than the tracial
mode. As a main motivation to study CLT in such generality on small mesoscopic
scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis
(Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps
with any deterministic matrix are asymptotically Gaussian after a small spectral
averaging. Finally, in the macroscopic regime our result also generalizes (Zh.
Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover
ensembles in between. The main technical inputs are the recent\r\nmultiresolvent
local laws with traceless deterministic matrices from the companion paper (Comm.
Math. Phys. 388 (2021) 1005–1048)."
acknowledgement: The second author is partially funded by the ERC Advanced Grant “RMTBEYOND”
No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner
Foundation and the ETH Zürich Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner
matrices. Annals of Applied Probability. 2023;33(1):447-489. doi:10.1214/22-AAP1820
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Functional central
limit theorems for Wigner matrices. Annals of Applied Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/22-AAP1820
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central
Limit Theorems for Wigner Matrices.” Annals of Applied Probability. Institute
of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AAP1820.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems
for Wigner matrices,” Annals of Applied Probability, vol. 33, no. 1. Institute
of Mathematical Statistics, pp. 447–489, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems
for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.
mla: Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.”
Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical
Statistics, 2023, pp. 447–89, doi:10.1214/22-AAP1820.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023)
447–489.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-10-17T12:48:52Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/22-AAP1820
ec_funded: 1
external_id:
arxiv:
- '2012.13218'
isi:
- '000946432400015'
intvolume: ' 33'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.13218
month: '02'
oa: 1
oa_version: Preprint
page: 447-489
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Annals of Applied Probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional central limit theorems for Wigner matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '8682'
abstract:
- lang: eng
text: It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous
for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover,
for such varieties it follows from a general conjecture of Colliot-Thélène that
the Brauer--Manin obstruction to the Hasse principle should be the only one, so
that the Hasse principle is expected to hold. Working over the field of rational
numbers and ordering Fano hypersurfaces of fixed degree and dimension by height,
we prove that almost every such hypersurface satisfies the Hasse principle provided
that the dimension is at least 3. This proves a conjecture of Poonen and Voloch
in every case except for cubic surfaces.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Pierre Le
full_name: Boudec, Pierre Le
last_name: Boudec
- first_name: Will
full_name: Sawin, Will
last_name: Sawin
citation:
ama: Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces.
Annals of Mathematics. 2023;197(3):1115-1203. doi:10.4007/annals.2023.197.3.3
apa: Browning, T. D., Boudec, P. L., & Sawin, W. (2023). The Hasse principle
for random Fano hypersurfaces. Annals of Mathematics. Princeton University.
https://doi.org/10.4007/annals.2023.197.3.3
chicago: Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle
for Random Fano Hypersurfaces.” Annals of Mathematics. Princeton University,
2023. https://doi.org/10.4007/annals.2023.197.3.3.
ieee: T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random
Fano hypersurfaces,” Annals of Mathematics, vol. 197, no. 3. Princeton
University, pp. 1115–1203, 2023.
ista: Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano
hypersurfaces. Annals of Mathematics. 197(3), 1115–1203.
mla: Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.”
Annals of Mathematics, vol. 197, no. 3, Princeton University, 2023, pp.
1115–203, doi:10.4007/annals.2023.197.3.3.
short: T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.
date_created: 2020-10-19T14:28:50Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-17T12:47:43Z
day: '01'
department:
- _id: TiBr
doi: 10.4007/annals.2023.197.3.3
external_id:
arxiv:
- '2006.02356'
isi:
- '000966611000003'
intvolume: ' 197'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.02356
month: '05'
oa: 1
oa_version: Preprint
page: 1115-1203
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/when-is-necessary-sufficient/
status: public
title: The Hasse principle for random Fano hypersurfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2023'
...
---
_id: '12706'
abstract:
- lang: eng
text: Allometric settings of population dynamics models are appealing due to their
parsimonious nature and broad utility when studying system level effects. Here,
we parameterise the size-scaled Rosenzweig-MacArthur differential equations to
eliminate prey-mass dependency, facilitating an in depth analytic study of the
equations which incorporates scaling parameters’ contributions to coexistence.
We define the functional response term to match empirical findings, and examine
situations where metabolic theory derivations and observation diverge. The dynamical
properties of the Rosenzweig-MacArthur system, encompassing the distribution of
size-abundance equilibria, the scaling of period and amplitude of population cycling,
and relationships between predator and prey abundances, are consistent with empirical
observation. Our parameterisation is an accurate minimal model across 15+ orders
of mass magnitude.
acknowledgement: "This research was supported by an Australian Government Research
Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is
supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program.
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Jody C.
full_name: Mckerral, Jody C.
last_name: Mckerral
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Vladimir
full_name: Ejov, Vladimir
last_name: Ejov
- first_name: Louise
full_name: Bartle, Louise
last_name: Bartle
- first_name: James G.
full_name: Mitchell, James G.
last_name: Mitchell
- first_name: Jerzy A.
full_name: Filar, Jerzy A.
last_name: Filar
citation:
ama: Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical
parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur
equations. PLoS One. 2023;18(2):e0279838. doi:10.1371/journal.pone.0279838
apa: Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., &
Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the
allometric Rosenzweig-MacArthur equations. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0279838
chicago: Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James
G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis
of the Allometric Rosenzweig-MacArthur Equations.” PLoS One. Public Library
of Science, 2023. https://doi.org/10.1371/journal.pone.0279838.
ieee: J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A.
Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur
equations,” PLoS One, vol. 18, no. 2. Public Library of Science, p. e0279838,
2023.
ista: Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical
parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur
equations. PLoS One. 18(2), e0279838.
mla: Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis
of the Allometric Rosenzweig-MacArthur Equations.” PLoS One, vol. 18, no.
2, Public Library of Science, 2023, p. e0279838, doi:10.1371/journal.pone.0279838.
short: J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar,
PLoS One 18 (2023) e0279838.
date_created: 2023-03-05T23:01:05Z
date_published: 2023-02-27T00:00:00Z
date_updated: 2023-10-17T12:53:30Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0279838
external_id:
isi:
- '000996122900022'
pmid:
- '36848357'
file:
- access_level: open_access
checksum: 798ed5739a4117b03173e5d56e0534c9
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T10:26:45Z
date_updated: 2023-03-07T10:26:45Z
file_id: '12712'
file_name: 2023_PLOSOne_Mckerral.pdf
file_size: 1257003
relation: main_file
success: 1
file_date_updated: 2023-03-07T10:26:45Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: e0279838
pmid: 1
publication: PLoS One
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur
equations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '13202'
abstract:
- lang: eng
text: Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role
in neuronal activities through interaction with various proteins involved in signaling
at membranes. However, the distribution pattern of PI(4,5)P2 and the association
with these proteins on the neuronal cell membranes remain elusive. In this study,
we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture
replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution
of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters
with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal
membranes in male C57BL/6J mice. These clusters show preferential accumulation
in specific membrane compartments of different cell types, in particular, in Purkinje
cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore,
we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different
membrane compartments, whereas its association with mGluR1α was compartment specific.
These results suggest that our SDS-FRL method provides valuable insights into
the physiological functions of PI(4,5)P2 in neurons.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: This work was supported by The Institute of Science and Technology
(IST) Austria, the European Union's Horizon 2020 Research and Innovation Program
under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the
European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta
Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample
preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria)
for technical support with EM works, Natalia Baranova (University of Vienna, Vienna,
Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome
preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments.
article_processing_charge: No
article_type: original
author:
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution
on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience.
2023;43(23):4197-4216. doi:10.1523/JNEUROSCI.1514-22.2023
apa: Eguchi, K., Le Monnier, E., & Shigemoto, R. (2023). Nanoscale phosphoinositide
distribution on cell membranes of mouse cerebellar neurons. The Journal of
Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1514-22.2023
chicago: Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide
Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of
Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.1514-22.2023.
ieee: K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution
on cell membranes of mouse cerebellar neurons,” The Journal of Neuroscience,
vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023.
ista: Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution
on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23),
4197–4216.
mla: Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes
of Mouse Cerebellar Neurons.” The Journal of Neuroscience, vol. 43, no.
23, Society for Neuroscience, 2023, pp. 4197–216, doi:10.1523/JNEUROSCI.1514-22.2023.
short: K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023)
4197–4216.
date_created: 2023-07-09T22:01:12Z
date_published: 2023-06-07T00:00:00Z
date_updated: 2023-10-18T07:12:47Z
day: '07'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.1514-22.2023
ec_funded: 1
external_id:
isi:
- '001020132100005'
pmid:
- '37160366'
file:
- access_level: open_access
checksum: 70b2141870e0bf1c94fd343e18fdbc32
content_type: application/pdf
creator: alisjak
date_created: 2023-07-10T09:04:58Z
date_updated: 2023-07-10T09:04:58Z
file_id: '13205'
file_name: 2023_JN_Eguchi.pdf
file_size: 7794425
relation: main_file
success: 1
file_date_updated: 2023-07-10T09:04:58Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 4197-4216
pmid: 1
project:
- _id: 2659CC84-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '793482'
name: 'Ultrastructural analysis of phosphoinositides in nerve terminals: distribution,
dynamics and physiological roles in synaptic transmission'
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar
neurons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2023'
...
---
_id: '12916'
abstract:
- lang: eng
text: "We apply a variant of the square-sieve to produce an upper bound for the
number of rational points of bounded height on a family of surfaces that admit
a fibration over P1 whose general fibre is a hyperelliptic curve. The implied
constant does not depend on the coefficients of the polynomial defining the surface.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Dante
full_name: Bonolis, Dante
id: 6A459894-5FDD-11E9-AF35-BB24E6697425
last_name: Bonolis
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
2023;24(1):173-204. doi:10.2422/2036-2145.202010_018
apa: Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points
on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018
chicago: Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023.
https://doi.org/10.2422/2036-2145.202010_018.
ieee: D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic
fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze,
vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204,
2023.
ista: Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
24(1), 173–204.
mla: Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della
Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018.
short: D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze 24 (2023) 173–204.
date_created: 2023-05-07T22:01:04Z
date_published: 2023-02-16T00:00:00Z
date_updated: 2023-10-18T06:54:30Z
day: '16'
department:
- _id: TiBr
doi: 10.2422/2036-2145.202010_018
external_id:
arxiv:
- '2007.14182'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2007.14182
month: '02'
oa: 1
oa_version: Preprint
page: 173-204
publication: Annali della Scuola Normale Superiore di Pisa - Classe di Scienze
publication_identifier:
eissn:
- 2036-2145
issn:
- 0391-173X
publication_status: published
publisher: Scuola Normale Superiore - Edizioni della Normale
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uniform bounds for rational points on hyperelliptic fibrations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '14422'
abstract:
- lang: eng
text: "Animals exhibit a remarkable ability to learn and remember new behaviors,
skills, and associations throughout their lifetime. These capabilities are made
possible thanks to a variety of\r\nchanges in the brain throughout adulthood,
regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons—
and specifically changes in the connections between neurons, the\r\nsynapses,
were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom
past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity.
Understanding how a myriad of biochemical processes operating at individual\r\nsynapses
can somehow work in concert to give rise to meaningful changes in behavior is
a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental
search for the precise plasticity mechanisms at play in the brain\r\nis daunting,
as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches
have thus been the default method to probe the plasticity-behavior connection.
Such\r\nstudies attempt to extract unifying principles across synapses and model
all observed synaptic\r\nchanges using plasticity rules: equations that govern
the evolution of synaptic strengths across\r\ntime in neuronal network models.
These rules can use many relevant quantities to determine\r\nthe magnitude of
synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction
potentials, the recent neuronal activity levels, the state of neighboring synapses,
etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced
to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis,
we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe
explore whether a numerical approach could automatically discover the plasticity
rules\r\nthat elicit desired behaviors in large networks of interconnected neurons.
This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity
rules which themselves will make\r\nneuronal networks learn how to solve a desired
task. We first write all the potential plasticity\r\nmechanisms to consider using
a single expression with adjustable parameters. We then optimize\r\nthese plasticity
parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto
involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe
show that these automated approaches are powerful tools, able to complement established\r\nanalytical
methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic,
spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity
rules that reliably elicit memory-related behaviors. Our approaches allow for
more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies
of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity
in spiking network models.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
citation:
ama: 'Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422'
apa: 'Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity
rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422'
chicago: 'Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.'
ieee: 'B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute
of Science and Technology Austria, 2023.'
ista: 'Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules.
Institute of Science and Technology Austria.'
mla: 'Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.'
short: 'B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute
of Science and Technology Austria, 2023.'
date_created: 2023-10-12T14:13:25Z
date_published: 2023-10-12T00:00:00Z
date_updated: 2023-10-18T09:20:56Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TiVo
doi: 10.15479/at:ista:14422
ec_funded: 1
file:
- access_level: closed
checksum: 7f636555eae7803323df287672fd13ed
content_type: application/pdf
creator: cchlebak
date_created: 2023-10-12T14:53:50Z
date_updated: 2023-10-12T14:54:52Z
embargo: 2024-10-12
embargo_to: open_access
file_id: '14424'
file_name: Confavreux_Thesis_2A.pdf
file_size: 30599717
relation: main_file
- access_level: closed
checksum: 725e85946db92290a4583a0de9779e1b
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-10-18T07:38:34Z
date_updated: 2023-10-18T07:56:08Z
file_id: '14440'
file_name: Confavreux Thesis.zip
file_size: 68406739
relation: source_file
file_date_updated: 2023-10-18T07:56:08Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '10'
oa_version: Published Version
page: '148'
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9633'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
title: 'Synapseek: Meta-learning synaptic plasticity rules'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14374'
abstract:
- lang: eng
text: "Superconductivity has many important applications ranging from levitating
trains over qubits to MRI scanners. The phenomenon is successfully modeled by
Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory
has been studied extensively for systems without boundary. However, little is
known in the presence of boundaries. With the help of numerical methods physicists
observed that the critical temperature may increase in the presence of a boundary.
The goal of this thesis is to understand the influence of boundaries on the critical
temperature in BCS theory and to give a first rigorous justification of these
observations. On the way, we also study two-body Schrödinger operators on domains
with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS
theory is based on a non-linear functional, where the minimizer indicates whether
the system is superconducting or in the normal, non-superconducting state. By
considering the Hessian of the BCS functional at the normal state, one can analyze
whether the normal state is possibly a minimum of the BCS functional and estimate
the critical temperature. The Hessian turns out to be a linear operator resembling
a Schrödinger operator for two interacting particles, but with more complicated
kinetic energy. As a first step, we study the two-body Schrödinger operator in
the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that
the addition of a boundary can create new eigenvalues, which correspond to the
two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need
to understand superconductivity in the translation invariant setting. While in
three dimensions this has been extensively studied, there is no mathematical literature
for the one and two dimensional cases. In dimensions one and two, we compute the
weak coupling asymptotics of the critical temperature and the energy gap in the
translation invariant setting. We also prove that their ratio is independent of
the microscopic details of the model in the weak coupling limit; this property
is referred to as universality.\r\n\r\nIn the third part, we study the critical
temperature of superconductors in the presence of boundaries. We start by considering
the one-dimensional case of a half-line with contact interaction. Then, we generalize
the results to generic interactions and half-spaces in one, two and three dimensions.
Finally, we compare the critical temperature of a quarter space in two dimensions
to the critical temperatures of a half-space and of the full space."
alternative_title:
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author:
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full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
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orcid: 0000-0002-9071-5880
citation:
ama: Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374
apa: Roos, B. (2023). Boundary superconductivity in BCS theory. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374
chicago: Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.
ieee: B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science
and Technology Austria, 2023.
ista: Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science
and Technology Austria.
mla: Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of
Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.
short: B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and
Technology Austria, 2023.
date_created: 2023-09-28T14:23:04Z
date_published: 2023-09-30T00:00:00Z
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call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
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grant_number: I06427
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full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: Boundary superconductivity in BCS theory
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short: CC BY-NC-SA (4.0)
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...
---
_id: '13207'
abstract:
- lang: eng
text: We consider the linear BCS equation, determining the BCS critical temperature,
in the presence of a boundary, where Dirichlet boundary conditions are imposed.
In the one-dimensional case with point interactions, we prove that the critical
temperature is strictly larger than the bulk value, at least at weak coupling.
In particular, the Cooper-pair wave function localizes near the boundary, an effect
that cannot be modeled by effective Neumann boundary conditions on the order parameter
as often imposed in Ginzburg–Landau theory. We also show that the relative shift
in critical temperature vanishes if the coupling constant either goes to zero
or to infinity.
acknowledgement: We thank Egor Babaev for encouraging us to study this problem, and
Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the
European Union’s Horizon 2020 research and innovation programme under the ERC grant
agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.
article_processing_charge: No
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author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model.
Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439
apa: Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity
in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439
chicago: Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity
in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439.
ieee: C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS
model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540,
2023.
ista: Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS
model. Journal of Spectral Theory. 12(4), 1507–1540.
mla: Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal
of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439.
short: C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.
date_created: 2023-07-10T16:35:45Z
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department:
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- _id: RoSe
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publication: Journal of Spectral Theory
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type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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year: '2023'
...
---
_id: '14452'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and an environmental component, and the genetic component of
offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the parental
traits. In previous work, we showed that when trait values are determined by the
sum of a large number of additive Mendelian factors, each of small effect, one
can justify the infinitesimal model as a limit of Mendelian inheritance. In this
paper, we show that this result extends to include dominance. We define the model
in terms of classical quantities of quantitative genetics, before justifying it
as a limit of Mendelian inheritance as the number, M, of underlying loci tends
to infinity. As in the additive case, the multivariate normal distribution of
trait values across the pedigree can be expressed in terms of variance components
in an ancestral population and probabilities of identity by descent determined
by the pedigree. Now, with just first-order dominance effects, we require two-,
three-, and four-way identities. We also show that, even if we condition on parental
trait values, the “shared” and “residual” components of trait values within each
family will be asymptotically normally distributed as the number of loci tends
to infinity, with an error of order 1/M−−√. We illustrate our results with some
numerical examples.
acknowledgement: NHB was supported in part by ERC Grants 250152 and 101055327. AV
was partly supported by the chaire Modélisation Mathématique et Biodiversité of
Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation
X.
article_number: iyad133
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- 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: Alison M.
full_name: Etheridge, Alison M.
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics.
2023;225(2). doi:10.1093/genetics/iyad133
apa: Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal
model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133
chicago: Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal
Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133.
ieee: N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with
dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.
ista: Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance.
Genetics. 225(2), iyad133.
mla: Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics,
vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.
short: N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-30T13:04:11Z
day: '01'
ddc:
- '570'
department:
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doi: 10.1093/genetics/iyad133
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grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
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grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
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publisher: Oxford Academic
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volume: 225
year: '2023'
...
---
_id: '12949'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and a non-genetic (environmental) component and the genetic component
of offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the trait
values of the parents. Although the trait distribution across the whole population
can be far from normal, the trait distributions within families are normally distributed
with a variance-covariance matrix that is determined entirely by that in the
ancestral population and the probabilities of identity determined by the pedigree.
Moreover, conditioning on some of the trait values within the pedigree has predictable
effects on the mean and variance within and between families. In previous work,
Barton et al. (2017), we showed that when trait values are determined by the sum
of a large number of Mendelian factors, each of small effect, one can justify
the infinitesimal model as limit of Mendelian inheritance. It was also shown that
under some forms of epistasis, trait values within a family are still normally
distributed.
article_processing_charge: No
author:
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full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949
apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949
chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.
ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science
and Technology Austria, 2023.
ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:12949.
mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute
of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.
short: N.H. Barton, (2023).
contributor:
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first_name: Amandine
last_name: Veber
- contributor_type: researcher
first_name: Alison
last_name: Etheridge
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keyword:
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...
---
_id: '14461'
abstract:
- lang: eng
text: 'Communication-reduction techniques are a popular way to improve scalability
in data-parallel training of deep neural networks (DNNs). The recent emergence
of large language models such as GPT has created the need for new approaches to
exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training
is highly popular, yet it still encounters scalability bottlenecks. One reason
is that applying compression techniques to FSDP is challenging: as the vast majority
of the communication involves the model’s weights, direct compression alters convergence
and leads to accuracy loss. We present QSDP, a variant of FSDP which supports
both gradient and weight quantization with theoretical guarantees, is simple to
implement and has essentially no overheads. To derive QSDP we prove that a natural
modification of SGD achieves convergence even when we only maintain quantized
weights, and thus the domain over which we train consists of quantized points
and is, therefore, highly non-convex. We validate this approach by training GPT-family
models with up to 1.3 billion parameters on a multi-node cluster. Experiments
show that QSDP preserves model accuracy, while completely removing the communication
bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors gratefully acknowledge funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML), as well as experimental support from the IST
Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois
Schloegl. AV acknowledges the support of the French Agence Nationale de la Recherche
(ANR), under grant ANR-21-CE48-0016 (project COMCOPT), the support of Fondation
Hadamard with a PRMO grant, and the support of CNRS with a CoopIntEER IEA grant
(project ALFRED).
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Ilia
full_name: Markov, Ilia
id: D0CF4148-C985-11E9-8066-0BDEE5697425
last_name: Markov
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
- first_name: Qi
full_name: Guo, Qi
last_name: Guo
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Markov I, Vladu A, Guo Q, Alistarh D-A. Quantized distributed training of
large models with convergence guarantees. In: Proceedings of the 40th International
Conference on Machine Learning. Vol 202. ML Research Press; 2023:24020-24044.'
apa: 'Markov, I., Vladu, A., Guo, Q., & Alistarh, D.-A. (2023). Quantized distributed
training of large models with convergence guarantees. In Proceedings of the
40th International Conference on Machine Learning (Vol. 202, pp. 24020–24044).
Honolulu, Hawaii, HI, United States: ML Research Press.'
chicago: Markov, Ilia, Adrian Vladu, Qi Guo, and Dan-Adrian Alistarh. “Quantized
Distributed Training of Large Models with Convergence Guarantees.” In Proceedings
of the 40th International Conference on Machine Learning, 202:24020–44. ML
Research Press, 2023.
ieee: I. Markov, A. Vladu, Q. Guo, and D.-A. Alistarh, “Quantized distributed training
of large models with convergence guarantees,” in Proceedings of the 40th International
Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023,
vol. 202, pp. 24020–24044.
ista: 'Markov I, Vladu A, Guo Q, Alistarh D-A. 2023. Quantized distributed training
of large models with convergence guarantees. Proceedings of the 40th International
Conference on Machine Learning. ICML: International Conference on Machine Learning,
PMLR, vol. 202, 24020–24044.'
mla: Markov, Ilia, et al. “Quantized Distributed Training of Large Models with Convergence
Guarantees.” Proceedings of the 40th International Conference on Machine Learning,
vol. 202, ML Research Press, 2023, pp. 24020–44.
short: I. Markov, A. Vladu, Q. Guo, D.-A. Alistarh, in:, Proceedings of the 40th
International Conference on Machine Learning, ML Research Press, 2023, pp. 24020–24044.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:40:45Z
day: '30'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2302.02390'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.02390
month: '07'
oa: 1
oa_version: Preprint
page: 24020-24044
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantized distributed training of large models with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14462'
abstract:
- lang: eng
text: "We study fine-grained error bounds for differentially private algorithms
for counting under continual observation. Our main insight is that the matrix
mechanism when using lower-triangular matrices can be used in the continual observation
model. More specifically, we give an explicit factorization for the counting matrix
Mcount and upper bound the error explicitly. We also give a fine-grained analysis,
specifying the exact constant in the upper bound. Our analysis is based on upper
and lower bounds of the completely bounded norm (cb-norm) of Mcount\r\n. Along
the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal
on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large
range of the dimension of Mcount. Furthermore, we are the first to give concrete
error bounds for various problems under continual observation such as binary counting,
maintaining a histogram, releasing an approximately cut-preserving synthetic graph,
many graph-based statistics, and substring and episode counting. Finally, we note
that our result can be used to get a fine-grained error bound for non-interactive
local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private
counting under continual observation. Subsequent to this work, Henzinger et al.
(SODA, 2023) showed that our factorization also achieves fine-grained mean-squared
error."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the Austrian Science Fund (FWF) project Z 422-N, and project
“Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. 2020–2024. JU’s research was
funded by Decanal Research Grant. A part of this work was done when JU was visiting
Indian Statistical Institute, Delhi. The authors would like to thank Rajat Bhatia,
Aleksandar Nikolov, Shanta Laisharam, Vern Paulsen, Ryan Rogers, Abhradeep Thakurta,
and Sarvagya Upadhyay for useful discussions."
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Hendrik
full_name: Fichtenberger, Hendrik
last_name: Fichtenberger
- 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: Jalaj
full_name: Upadhyay, Jalaj
last_name: Upadhyay
citation:
ama: 'Fichtenberger H, Henzinger MH, Upadhyay J. Constant matters: Fine-grained
error bound on differentially private continual observation. In: Proceedings
of the 40th International Conference on Machine Learning. Vol 202. ML Research
Press; 2023:10072-10092.'
apa: 'Fichtenberger, H., Henzinger, M. H., & Upadhyay, J. (2023). Constant matters:
Fine-grained error bound on differentially private continual observation. In Proceedings
of the 40th International Conference on Machine Learning (Vol. 202, pp. 10072–10092).
Honolulu, Hawaii, HI, United States: ML Research Press.'
chicago: 'Fichtenberger, Hendrik, Monika H Henzinger, and Jalaj Upadhyay. “Constant
Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.”
In Proceedings of the 40th International Conference on Machine Learning,
202:10072–92. ML Research Press, 2023.'
ieee: 'H. Fichtenberger, M. H. Henzinger, and J. Upadhyay, “Constant matters: Fine-grained
error bound on differentially private continual observation,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, Hawaii,
HI, United States, 2023, vol. 202, pp. 10072–10092.'
ista: 'Fichtenberger H, Henzinger MH, Upadhyay J. 2023. Constant matters: Fine-grained
error bound on differentially private continual observation. Proceedings of the
40th International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 202, 10072–10092.'
mla: 'Fichtenberger, Hendrik, et al. “Constant Matters: Fine-Grained Error Bound
on Differentially Private Continual Observation.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10072–92.'
short: H. Fichtenberger, M.H. Henzinger, J. Upadhyay, in:, Proceedings of the 40th
International Conference on Machine Learning, ML Research Press, 2023, pp. 10072–10092.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:54:05Z
day: '30'
department:
- _id: MoHe
ec_funded: 1
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.mlr.press/v202/fichtenberger23a/fichtenberger23a.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 10072-10092
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Wittgenstein Award - Monika Henzinger
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Constant matters: Fine-grained error bound on differentially private continual
observation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14459'
abstract:
- lang: eng
text: Autoencoders are a popular model in many branches of machine learning and
lossy data compression. However, their fundamental limits, the performance of
gradient methods and the features learnt during optimization remain poorly understood,
even in the two-layer setting. In fact, earlier work has considered either linear
autoencoders or specific training regimes (leading to vanishing or diverging compression
rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders
trained in the challenging proportional regime in which the input dimension scales
linearly with the size of the representation. Our results characterize the minimizers
of the population risk, and show that such minimizers are achieved by gradient
methods; their structure is also unveiled, thus leading to a concise description
of the features obtained via training. For the special case of a sign activation
function, our analysis establishes the fundamental limits for the lossy compression
of Gaussian sources via (shallow) autoencoders. Finally, while the results are
proved for Gaussian data, numerical simulations on standard datasets display the
universality of the theoretical predictions.
acknowledgement: Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported
by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF
CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science
(EnCORE).
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Kevin
full_name: Kögler, Kevin
id: 94ec913c-dc85-11ea-9058-e5051ab2428b
last_name: Kögler
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer
autoencoders, and achieving them with gradient methods. In: Proceedings of
the 40th International Conference on Machine Learning. Vol 202. ML Research
Press; 2023:31151-31209.'
apa: 'Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental
limits of two-layer autoencoders, and achieving them with gradient methods. In
Proceedings of the 40th International Conference on Machine Learning (Vol.
202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.'
chicago: Shevchenko, Aleksandr, Kevin Kögler, Hamed Hassani, and Marco Mondelli.
“Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient
Methods.” In Proceedings of the 40th International Conference on Machine Learning,
202:31151–209. ML Research Press, 2023.
ieee: A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits
of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, Hawaii,
HI, United States, 2023, vol. 202, pp. 31151–31209.
ista: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of
two-layer autoencoders, and achieving them with gradient methods. Proceedings
of the 40th International Conference on Machine Learning. ICML: International
Conference on Machine Learning, PMLR, vol. 202, 31151–31209.'
mla: Shevchenko, Aleksandr, et al. “Fundamental Limits of Two-Layer Autoencoders,
and Achieving Them with Gradient Methods.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209.
short: A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the
40th International Conference on Machine Learning, ML Research Press, 2023, pp.
31151–31209.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T08:52:28Z
day: '30'
department:
- _id: MaMo
- _id: DaAl
external_id:
arxiv:
- '2212.13468'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.13468
month: '07'
oa: 1
oa_version: Preprint
page: 31151-31209
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fundamental limits of two-layer autoencoders, and achieving them with gradient
methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14460'
abstract:
- lang: eng
text: We provide an efficient implementation of the backpropagation algorithm, specialized
to the case where the weights of the neural network being trained are sparse.
Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and
common layer types (e.g., convolutional or linear). We provide a fast vectorized
implementation on commodity CPUs, and show that it can yield speedups in end-to-end
runtime experiments, both in transfer learning using already-sparsified networks,
and in training sparse networks from scratch. Thus, our results provide the first
support for sparse training on commodity hardware.
acknowledgement: 'We would like to thank Elias Frantar for his valuable assistance
and support at the outset of this project, and the anonymous ICML and SNN reviewers
for very constructive feedback. EI was supported in part by the FWF DK VGSCO, grant
agreement number W1260-N35. DA acknowledges generous ERC support, via Starting Grant
805223 ScaleML. '
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Mahdi
full_name: Nikdan, Mahdi
id: 66374281-f394-11eb-9cf6-869147deecc0
last_name: Nikdan
- first_name: Tommaso
full_name: Pegolotti, Tommaso
last_name: Pegolotti
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. SparseProp: Efficient
sparse backpropagation for faster training of neural networks at the edge. In:
Proceedings of the 40th International Conference on Machine Learning. Vol
202. ML Research Press; 2023:26215-26227.'
apa: 'Nikdan, M., Pegolotti, T., Iofinova, E. B., Kurtic, E., & Alistarh, D.-A.
(2023). SparseProp: Efficient sparse backpropagation for faster training of neural
networks at the edge. In Proceedings of the 40th International Conference on
Machine Learning (Vol. 202, pp. 26215–26227). Honolulu, Hawaii, HI, United
States: ML Research Press.'
chicago: 'Nikdan, Mahdi, Tommaso Pegolotti, Eugenia B Iofinova, Eldar Kurtic, and
Dan-Adrian Alistarh. “SparseProp: Efficient Sparse Backpropagation for Faster
Training of Neural Networks at the Edge.” In Proceedings of the 40th International
Conference on Machine Learning, 202:26215–27. ML Research Press, 2023.'
ieee: 'M. Nikdan, T. Pegolotti, E. B. Iofinova, E. Kurtic, and D.-A. Alistarh, “SparseProp:
Efficient sparse backpropagation for faster training of neural networks at the
edge,” in Proceedings of the 40th International Conference on Machine Learning,
Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 26215–26227.'
ista: 'Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. 2023. SparseProp:
Efficient sparse backpropagation for faster training of neural networks at the
edge. Proceedings of the 40th International Conference on Machine Learning. ICML:
International Conference on Machine Learning, PMLR, vol. 202, 26215–26227.'
mla: 'Nikdan, Mahdi, et al. “SparseProp: Efficient Sparse Backpropagation for Faster
Training of Neural Networks at the Edge.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 26215–27.'
short: M. Nikdan, T. Pegolotti, E.B. Iofinova, E. Kurtic, D.-A. Alistarh, in:, Proceedings
of the 40th International Conference on Machine Learning, ML Research Press, 2023,
pp. 26215–26227.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:33:51Z
day: '30'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2302.04852'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.04852
month: '07'
oa: 1
oa_version: Preprint
page: 26215-26227
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SparseProp: Efficient sparse backpropagation for faster training of neural
networks at the edge'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14457'
abstract:
- lang: eng
text: "Threshold secret sharing allows a dealer to split a secret s into n shares,
such that any t shares allow for reconstructing s, but no t-1 shares reveal any
information about s. Leakage-resilient secret sharing requires that the secret
remains hidden, even when an adversary additionally obtains a limited amount of
leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret
sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n
and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen
and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving
that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n).\r\nIn
this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy
leakage-resilience, where a random subset of leakages is replaced by uniformly
random noise. We prove a lower bound for Shamir’s secret sharing, similar to that
of Nielsen and Simkin, which holds even when a constant fraction of leakages is
replaced by random noise. To this end, we first prove a lower bound on the share
size of any noisy-leakage-resilient sharing scheme. We then use this lower bound
to show that there exist universal constants c1, c2, such that for sufficiently
large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient
for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random
noise.\r\n\r\n\r\n\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Charlotte
full_name: Hoffmann, Charlotte
id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7
last_name: Hoffmann
orcid: 0000-0003-2027-5549
- first_name: Mark
full_name: Simkin, Mark
last_name: Simkin
citation:
ama: 'Hoffmann C, Simkin M. Stronger lower bounds for leakage-resilient secret sharing.
In: 8th International Conference on Cryptology and Information Security in
Latin America. Vol 14168. Springer Nature; 2023:215-228. doi:10.1007/978-3-031-44469-2_11'
apa: 'Hoffmann, C., & Simkin, M. (2023). Stronger lower bounds for leakage-resilient
secret sharing. In 8th International Conference on Cryptology and Information
Security in Latin America (Vol. 14168, pp. 215–228). Quito, Ecuador: Springer
Nature. https://doi.org/10.1007/978-3-031-44469-2_11'
chicago: Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient
Secret Sharing.” In 8th International Conference on Cryptology and Information
Security in Latin America, 14168:215–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44469-2_11.
ieee: C. Hoffmann and M. Simkin, “Stronger lower bounds for leakage-resilient secret
sharing,” in 8th International Conference on Cryptology and Information Security
in Latin America, Quito, Ecuador, 2023, vol. 14168, pp. 215–228.
ista: 'Hoffmann C, Simkin M. 2023. Stronger lower bounds for leakage-resilient secret
sharing. 8th International Conference on Cryptology and Information Security in
Latin America. LATINCRYPT: Conference on Cryptology and Information Security in
Latin America, LNCS, vol. 14168, 215–228.'
mla: Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient
Secret Sharing.” 8th International Conference on Cryptology and Information
Security in Latin America, vol. 14168, Springer Nature, 2023, pp. 215–28,
doi:10.1007/978-3-031-44469-2_11.
short: C. Hoffmann, M. Simkin, in:, 8th International Conference on Cryptology and
Information Security in Latin America, Springer Nature, 2023, pp. 215–228.
conference:
end_date: 2023-10-06
location: Quito, Ecuador
name: 'LATINCRYPT: Conference on Cryptology and Information Security in Latin America'
start_date: 2023-10-03
date_created: 2023-10-29T23:01:16Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-31T11:43:12Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-031-44469-2_11
intvolume: ' 14168'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/1017
month: '10'
oa: 1
oa_version: Preprint
page: 215-228
publication: 8th International Conference on Cryptology and Information Security in
Latin America
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031444685'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stronger lower bounds for leakage-resilient secret sharing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14168
year: '2023'
...
---
_id: '14458'
abstract:
- lang: eng
text: 'We show for the first time that large-scale generative pretrained transformer
(GPT) family models can be pruned to at least 50% sparsity in one-shot, without
any retraining, at minimal loss of accuracy. This is achieved via a new pruning
method called SparseGPT, specifically designed to work efficiently and accurately
on massive GPT-family models. We can execute SparseGPT on the largest available
open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach
60% unstructured sparsity with negligible increase in perplexity: remarkably,
more than 100 billion weights from these models can be ignored at inference time.
SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible
with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors gratefully acknowledge funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement
No. 805223 ScaleML), as well as experimental support from Eldar Kurtic, and from
the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and
Alois Schloegl.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Frantar E, Alistarh D-A. SparseGPT: Massive language models can be accurately
pruned in one-shot. In: Proceedings of the 40th International Conference on
Machine Learning. Vol 202. ML Research Press; 2023:10323-10337.'
apa: 'Frantar, E., & Alistarh, D.-A. (2023). SparseGPT: Massive language models
can be accurately pruned in one-shot. In Proceedings of the 40th International
Conference on Machine Learning (Vol. 202, pp. 10323–10337). Honolulu, Hawaii,
HI, United States: ML Research Press.'
chicago: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language
Models Can Be Accurately Pruned in One-Shot.” In Proceedings of the 40th International
Conference on Machine Learning, 202:10323–37. ML Research Press, 2023.'
ieee: 'E. Frantar and D.-A. Alistarh, “SparseGPT: Massive language models can be
accurately pruned in one-shot,” in Proceedings of the 40th International Conference
on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202,
pp. 10323–10337.'
ista: 'Frantar E, Alistarh D-A. 2023. SparseGPT: Massive language models can be
accurately pruned in one-shot. Proceedings of the 40th International Conference
on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
vol. 202, 10323–10337.'
mla: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models
Can Be Accurately Pruned in One-Shot.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10323–37.'
short: E. Frantar, D.-A. Alistarh, in:, Proceedings of the 40th International Conference
on Machine Learning, ML Research Press, 2023, pp. 10323–10337.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:16Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:59:42Z
day: '30'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2301.00774'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.00774
month: '07'
oa: 1
oa_version: Preprint
page: 10323-10337
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SparseGPT: Massive language models can be accurately pruned in one-shot'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14451'
abstract:
- lang: eng
text: 'We investigate the potential of Multi-Objective, Deep Reinforcement Learning
for stock and cryptocurrency single-asset trading: in particular, we consider
a Multi-Objective algorithm which generalizes the reward functions and discount
factor (i.e., these components are not specified a priori, but incorporated in
the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT,
XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of
the proposed Multi-Objective algorithm, and provide preliminary statistical evidence
showing increased predictive stability over the corresponding Single-Objective
strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge
over the corresponding Single-Objective strategy when the reward mechanism is
sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss
the generalization properties with respect to the discount factor. The entirety
of our code is provided in open-source format.'
acknowledgement: Open access funding provided by Università degli Studi di Trieste
within the CRUI-CARE Agreement. Funding was provided by Austrian Science Fund (Grant
No. F65), Horizon 2020 (Grant No. 754411) and Österreichische Forschungsförderungsgesellschaft.
article_processing_charge: Yes (via OA deal)
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: Constantin
full_name: Disselkamp, Constantin
last_name: Disselkamp
- first_name: Davide
full_name: Scassola, Davide
last_name: Scassola
- first_name: Christopher
full_name: Helf, Christopher
last_name: Helf
citation:
ama: 'Cornalba F, Disselkamp C, Scassola D, Helf C. Multi-objective reward generalization:
improving performance of Deep Reinforcement Learning for applications in single-asset
trading. Neural Computing and Applications. 2023. doi:10.1007/s00521-023-09033-7'
apa: 'Cornalba, F., Disselkamp, C., Scassola, D., & Helf, C. (2023). Multi-objective
reward generalization: improving performance of Deep Reinforcement Learning for
applications in single-asset trading. Neural Computing and Applications.
Springer Nature. https://doi.org/10.1007/s00521-023-09033-7'
chicago: 'Cornalba, Federico, Constantin Disselkamp, Davide Scassola, and Christopher
Helf. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement
Learning for Applications in Single-Asset Trading.” Neural Computing and Applications.
Springer Nature, 2023. https://doi.org/10.1007/s00521-023-09033-7.'
ieee: 'F. Cornalba, C. Disselkamp, D. Scassola, and C. Helf, “Multi-objective reward
generalization: improving performance of Deep Reinforcement Learning for applications
in single-asset trading,” Neural Computing and Applications. Springer Nature,
2023.'
ista: 'Cornalba F, Disselkamp C, Scassola D, Helf C. 2023. Multi-objective reward
generalization: improving performance of Deep Reinforcement Learning for applications
in single-asset trading. Neural Computing and Applications.'
mla: 'Cornalba, Federico, et al. “Multi-Objective Reward Generalization: Improving
Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.”
Neural Computing and Applications, Springer Nature, 2023, doi:10.1007/s00521-023-09033-7.'
short: F. Cornalba, C. Disselkamp, D. Scassola, C. Helf, Neural Computing and Applications
(2023).
date_created: 2023-10-22T22:01:16Z
date_published: 2023-10-05T00:00:00Z
date_updated: 2023-10-31T10:58:28Z
day: '05'
department:
- _id: JuFi
doi: 10.1007/s00521-023-09033-7
ec_funded: 1
external_id:
arxiv:
- '2203.04579'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00521-023-09033-7
month: '10'
oa: 1
oa_version: Published Version
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: Neural Computing and Applications
publication_identifier:
eissn:
- 1433-3058
issn:
- 0941-0643
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multi-objective reward generalization: improving performance of Deep Reinforcement
Learning for applications in single-asset trading'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14442'
abstract:
- lang: eng
text: In the presence of an obstacle, active particles condensate into a surface
“wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification
current arises in addition to wetting. Asymmetric geometries are therefore commonly
used to concentrate microorganisms like bacteria and sperms. However, most studies
neglect the fact that biological active matter is diverse, composed of individuals
with distinct self-propulsions. Using simulations, we study a mixture of “fast”
and “slow” active Brownian disks in two dimensions interacting with large half-disk
obstacles. With this prototypical obstacle geometry, we analyze how the stationary
collective behavior depends on the degree of self-propulsion “diversity,” defined
as proportional to the difference between the self-propulsion speeds, while keeping
the average self-propulsion speed fixed. A wetting layer rich in fast particles
arises. The rectification current is amplified by speed diversity due to a superlinear
dependence of rectification on self-propulsion speed, which arises from cooperative
effects. Thus, the total rectification current cannot be obtained from an effective
one-component active fluid with the same average self-propulsion speed, highlighting
the importance of considering diversity in active matter.
acknowledgement: MR-V and RS are supported by Fondecyt Grant No. 1220536 and Millennium
Science Initiative Program NCN19_170D of ANID, Chile. P.d.C. was supported by Scholarships
Nos. 2021/10139-2 and 2022/13872-5 and ICTP-SAIFR Grant No. 2021/14335-0, all granted
by São Paulo Research Foundation (FAPESP), Brazil.
article_number: '95'
article_processing_charge: No
article_type: original
author:
- first_name: Mauricio Nicolas
full_name: Rojas Vega, Mauricio Nicolas
id: 441e7207-f91f-11ec-b67c-9e6fe3d8fd6d
last_name: Rojas Vega
- first_name: Pablo
full_name: De Castro, Pablo
last_name: De Castro
- first_name: Rodrigo
full_name: Soto, Rodrigo
last_name: Soto
citation:
ama: Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting
with asymmetric obstacles. The European Physical Journal E. 2023;46(10).
doi:10.1140/epje/s10189-023-00354-y
apa: Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Mixtures of self-propelled
particles interacting with asymmetric obstacles. The European Physical Journal
E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00354-y
chicago: Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures
of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European
Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00354-y.
ieee: M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles
interacting with asymmetric obstacles,” The European Physical Journal E,
vol. 46, no. 10. Springer Nature, 2023.
ista: Rojas Vega MN, De Castro P, Soto R. 2023. Mixtures of self-propelled particles
interacting with asymmetric obstacles. The European Physical Journal E. 46(10),
95.
mla: Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles
Interacting with Asymmetric Obstacles.” The European Physical Journal E,
vol. 46, no. 10, 95, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00354-y.
short: M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46
(2023).
date_created: 2023-10-22T22:01:13Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-31T11:16:41Z
day: '01'
department:
- _id: AnSa
doi: 10.1140/epje/s10189-023-00354-y
external_id:
pmid:
- '37819444'
intvolume: ' 46'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
pmid: 1
publication: The European Physical Journal E
publication_identifier:
eissn:
- 1292-895X
issn:
- 1292-8941
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixtures of self-propelled particles interacting with asymmetric obstacles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_id: '14444'
abstract:
- lang: eng
text: "We prove several results about substructures in Latin squares. First, we
explain how to adapt our recent work on high-girth Steiner triple systems to the
setting of Latin squares, resolving a conjecture of Linial that there exist Latin
squares with arbitrarily high girth. As a consequence, we see that the number
of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare)
is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN\r\n
, where N is the number of intercalates in a uniformly random order- n Latin
square. \r\nIn fact, extending recent work of Kwan, Sah, and Sawhney, we resolve
the general large-deviation problem for intercalates in random Latin squares,
up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2))
and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)). \r\nFinally,
as an application of some new general tools for studying substructures in random
Latin squares, we show that in almost all order- n Latin squares, the number of
cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices
with the same arrangement of symbols) is of order n4, which is the minimum possible.
As observed by Gowers and Long, this number can be interpreted as measuring ``how
associative'' the quasigroup associated with the Latin square is."
acknowledgement: Sah and Sawhney were supported by NSF Graduate Research Fellowship
Program DGE-1745302. Sah was supported by the PD Soros Fellowship. Simkin was supported
by the Center of Mathematical Sciences and Applications at Harvard University.
article_processing_charge: Yes (in subscription journal)
article_type: original
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: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
- first_name: Michael
full_name: Simkin, Michael
last_name: Simkin
citation:
ama: Kwan MA, Sah A, Sawhney M, Simkin M. Substructures in Latin squares. Israel
Journal of Mathematics. 2023;256(2):363-416. doi:10.1007/s11856-023-2513-9
apa: Kwan, M. A., Sah, A., Sawhney, M., & Simkin, M. (2023). Substructures in
Latin squares. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2513-9
chicago: Kwan, Matthew Alan, Ashwin Sah, Mehtaab Sawhney, and Michael Simkin. “Substructures
in Latin Squares.” Israel Journal of Mathematics. Springer Nature, 2023.
https://doi.org/10.1007/s11856-023-2513-9.
ieee: M. A. Kwan, A. Sah, M. Sawhney, and M. Simkin, “Substructures in Latin squares,”
Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 363–416,
2023.
ista: Kwan MA, Sah A, Sawhney M, Simkin M. 2023. Substructures in Latin squares.
Israel Journal of Mathematics. 256(2), 363–416.
mla: Kwan, Matthew Alan, et al. “Substructures in Latin Squares.” Israel Journal
of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 363–416, doi:10.1007/s11856-023-2513-9.
short: M.A. Kwan, A. Sah, M. Sawhney, M. Simkin, Israel Journal of Mathematics 256
(2023) 363–416.
date_created: 2023-10-22T22:01:14Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-10-31T11:27:30Z
day: '01'
department:
- _id: MaKw
doi: 10.1007/s11856-023-2513-9
external_id:
arxiv:
- '2202.05088'
intvolume: ' 256'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2202.05088
month: '09'
oa: 1
oa_version: Preprint
page: 363-416
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Substructures in Latin squares
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 256
year: '2023'
...
---
_id: '14454'
abstract:
- lang: eng
text: As AI and machine-learned software are used increasingly for making decisions
that affect humans, it is imperative that they remain fair and unbiased in their
decisions. To complement design-time bias mitigation measures, runtime verification
techniques have been introduced recently to monitor the algorithmic fairness of
deployed systems. Previous monitoring techniques assume full observability of
the states of the (unknown) monitored system. Moreover, they can monitor only
fairness properties that are specified as arithmetic expressions over the probabilities
of different events. In this work, we extend fairness monitoring to systems modeled
as partially observed Markov chains (POMC), and to specifications containing arithmetic
expressions over the expected values of numerical functions on event sequences.
The only assumptions we make are that the underlying POMC is aperiodic and starts
in the stationary distribution, with a bound on its mixing time being known. These
assumptions enable us to estimate a given property for the entire distribution
of possible executions of the monitored POMC, by observing only a single execution.
Our monitors observe a long run of the system and, after each new observation,
output updated PAC-estimates of how fair or biased the system is. The monitors
are computationally lightweight and, using a prototype implementation, we demonstrate
their effectiveness on several real-world examples.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG 101020093.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Kueffner K, Mallik K. Monitoring algorithmic fairness under
partial observations. In: 23rd International Conference on Runtime Verification.
Vol 14245. Springer Nature; 2023:291-311. doi:10.1007/978-3-031-44267-4_15'
apa: 'Henzinger, T. A., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic
fairness under partial observations. In 23rd International Conference on Runtime
Verification (Vol. 14245, pp. 291–311). Thessaloniki, Greece: Springer Nature.
https://doi.org/10.1007/978-3-031-44267-4_15'
chicago: Henzinger, Thomas A, Konstantin Kueffner, and Kaushik Mallik. “Monitoring
Algorithmic Fairness under Partial Observations.” In 23rd International Conference
on Runtime Verification, 14245:291–311. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_15.
ieee: T. A. Henzinger, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness
under partial observations,” in 23rd International Conference on Runtime Verification,
Thessaloniki, Greece, 2023, vol. 14245, pp. 291–311.
ista: 'Henzinger TA, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness
under partial observations. 23rd International Conference on Runtime Verification.
RV: Conference on Runtime Verification, LNCS, vol. 14245, 291–311.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness under Partial
Observations.” 23rd International Conference on Runtime Verification, vol.
14245, Springer Nature, 2023, pp. 291–311, doi:10.1007/978-3-031-44267-4_15.
short: T.A. Henzinger, K. Kueffner, K. Mallik, in:, 23rd International Conference
on Runtime Verification, Springer Nature, 2023, pp. 291–311.
conference:
end_date: 2023-10-06
location: Thessaloniki, Greece
name: 'RV: Conference on Runtime Verification'
start_date: 2023-10-03
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-31T11:48:20Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-031-44267-4_15
ec_funded: 1
external_id:
arxiv:
- '2308.00341'
intvolume: ' 14245'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2308.00341
month: '10'
oa: 1
oa_version: Preprint
page: 291-311
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 23rd International Conference on Runtime Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031442667'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring algorithmic fairness under partial observations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14245
year: '2023'
...
---
_id: '14446'
abstract:
- lang: eng
text: Recent work has paid close attention to the first principle of Granger causality,
according to which cause precedes effect. In this context, the question may arise
whether the detected direction of causality also reverses after the time reversal
of unidirectionally coupled data. Recently, it has been shown that for unidirectionally
causally connected autoregressive (AR) processes X → Y, after time reversal of
data, the opposite causal direction Y → X is indeed detected, although typically
as part of the bidirectional X↔ Y link. As we argue here, the answer is different
when the measured data are not from AR processes but from linked deterministic
systems. When the goal is the usual forward data analysis, cross-mapping-like
approaches correctly detect X → Y, while Granger causality-like approaches, which
should not be used for deterministic time series, detect causal independence X
→ Y. The results of backward causal analysis depend on the predictability of the
reversed data. Unlike AR processes, observables from deterministic dynamical systems,
even complex nonlinear ones, can be predicted well forward, while backward predictions
can be difficult (notably when the time reversal of a function leads to one-to-many
relations). To address this problem, we propose an approach based on models that
provide multiple candidate predictions for the target, combined with a loss function
that consideres only the best candidate. The resulting good forward and backward
predictability supports the view that unidirectionally causally linked deterministic
dynamical systems X → Y can be expected to detect the same link both before and
after time reversal.
acknowledgement: The work was supported by the Scientific Grant Agency of the Ministry
of Education of the Slovak Republic and the Slovak Academy of Sciences, projects
APVV-21-0216, VEGA2-0096-21 and VEGA 2-0023-22.
article_processing_charge: Yes
article_type: original
author:
- first_name: Jozef
full_name: Jakubík, Jozef
last_name: Jakubík
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
- first_name: Martina
full_name: Chvosteková, Martina
last_name: Chvosteková
- first_name: Anna
full_name: Krakovská, Anna
last_name: Krakovská
citation:
ama: Jakubík J, Phuong M, Chvosteková M, Krakovská A. Against the flow of time with
multi-output models. Measurement Science Review. 2023;23(4):175-183. doi:10.2478/msr-2023-0023
apa: Jakubík, J., Phuong, M., Chvosteková, M., & Krakovská, A. (2023). Against
the flow of time with multi-output models. Measurement Science Review.
Sciendo. https://doi.org/10.2478/msr-2023-0023
chicago: Jakubík, Jozef, Mary Phuong, Martina Chvosteková, and Anna Krakovská. “Against
the Flow of Time with Multi-Output Models.” Measurement Science Review.
Sciendo, 2023. https://doi.org/10.2478/msr-2023-0023.
ieee: J. Jakubík, M. Phuong, M. Chvosteková, and A. Krakovská, “Against the flow
of time with multi-output models,” Measurement Science Review, vol. 23,
no. 4. Sciendo, pp. 175–183, 2023.
ista: Jakubík J, Phuong M, Chvosteková M, Krakovská A. 2023. Against the flow of
time with multi-output models. Measurement Science Review. 23(4), 175–183.
mla: Jakubík, Jozef, et al. “Against the Flow of Time with Multi-Output Models.”
Measurement Science Review, vol. 23, no. 4, Sciendo, 2023, pp. 175–83,
doi:10.2478/msr-2023-0023.
short: J. Jakubík, M. Phuong, M. Chvosteková, A. Krakovská, Measurement Science
Review 23 (2023) 175–183.
date_created: 2023-10-22T22:01:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-10-31T12:12:47Z
day: '01'
ddc:
- '510'
department:
- _id: ChLa
doi: 10.2478/msr-2023-0023
file:
- access_level: open_access
checksum: b069cc10fa6a7c96b2bc9f728165f9e6
content_type: application/pdf
creator: dernst
date_created: 2023-10-31T12:07:23Z
date_updated: 2023-10-31T12:07:23Z
file_id: '14476'
file_name: 2023_MeasurementScienceRev_Jakubik.pdf
file_size: 2639783
relation: main_file
success: 1
file_date_updated: 2023-10-31T12:07:23Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 175-183
publication: Measurement Science Review
publication_identifier:
eissn:
- 1335-8871
publication_status: published
publisher: Sciendo
quality_controlled: '1'
scopus_import: '1'
status: public
title: Against the flow of time with multi-output models
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2023'
...
---
_id: '14443'
abstract:
- lang: eng
text: "Importance Climate change, pollution, urbanization, socioeconomic inequality,
and psychosocial effects of the COVID-19 pandemic have caused massive changes
in environmental conditions that affect brain health during the life span, both
on a population level as well as on the level of the individual. How these environmental
factors influence the brain, behavior, and mental illness is not well known.\r\nObservations
\ A research strategy enabling population neuroscience to contribute to identify
brain mechanisms underlying environment-related mental illness by leveraging innovative
enrichment tools for data federation, geospatial observation, climate and pollution
measures, digital health, and novel data integration techniques is described.
This strategy can inform innovative treatments that target causal cognitive and
molecular mechanisms of mental illness related to the environment. An example
is presented of the environMENTAL Project that is leveraging federated cohort
data of over 1.5 million European citizens and patients enriched with deep phenotyping
data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms
related to environmental adversity underlying symptoms of depression, anxiety,
stress, and substance misuse.\r\nConclusions and Relevance This research will
lead to the development of objective biomarkers and evidence-based interventions
that will significantly improve outcomes of environment-related mental illness."
article_processing_charge: No
article_type: review
author:
- first_name: Gunter
full_name: Schumann, Gunter
last_name: Schumann
- first_name: Ole A.
full_name: Andreassen, Ole A.
last_name: Andreassen
- first_name: Tobias
full_name: Banaschewski, Tobias
last_name: Banaschewski
- first_name: Vince D.
full_name: Calhoun, Vince D.
last_name: Calhoun
- first_name: Nicholas
full_name: Clinton, Nicholas
last_name: Clinton
- first_name: Sylvane
full_name: Desrivieres, Sylvane
last_name: Desrivieres
- first_name: Ragnhild Eek
full_name: Brandlistuen, Ragnhild Eek
last_name: Brandlistuen
- first_name: Jianfeng
full_name: Feng, Jianfeng
last_name: Feng
- first_name: Soeren
full_name: Hese, Soeren
last_name: Hese
- first_name: Esther
full_name: Hitchen, Esther
last_name: Hitchen
- first_name: Per
full_name: Hoffmann, Per
last_name: Hoffmann
- first_name: Tianye
full_name: Jia, Tianye
last_name: Jia
- first_name: Viktor
full_name: Jirsa, Viktor
last_name: Jirsa
- first_name: Andre F.
full_name: Marquand, Andre F.
last_name: Marquand
- first_name: Frauke
full_name: Nees, Frauke
last_name: Nees
- first_name: Markus M.
full_name: Nöthen, Markus M.
last_name: Nöthen
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Elli
full_name: Polemiti, Elli
last_name: Polemiti
- first_name: Markus
full_name: Ralser, Markus
last_name: Ralser
- first_name: Michael
full_name: Rapp, Michael
last_name: Rapp
- first_name: Kerstin
full_name: Schepanski, Kerstin
last_name: Schepanski
- first_name: Tamara
full_name: Schikowski, Tamara
last_name: Schikowski
- first_name: Mel
full_name: Slater, Mel
last_name: Slater
- first_name: Peter
full_name: Sommer, Peter
last_name: Sommer
- first_name: Bernd Carsten
full_name: Stahl, Bernd Carsten
last_name: Stahl
- first_name: Paul M.
full_name: Thompson, Paul M.
last_name: Thompson
- first_name: Sven
full_name: Twardziok, Sven
last_name: Twardziok
- first_name: Dennis
full_name: Van Der Meer, Dennis
last_name: Van Der Meer
- first_name: Henrik
full_name: Walter, Henrik
last_name: Walter
- first_name: Lars
full_name: Westlye, Lars
last_name: Westlye
citation:
ama: 'Schumann G, Andreassen OA, Banaschewski T, et al. Addressing global environmental
challenges to mental health using population neuroscience: A review. JAMA Psychiatry.
2023;80(10):1066-1074. doi:10.1001/jamapsychiatry.2023.2996'
apa: 'Schumann, G., Andreassen, O. A., Banaschewski, T., Calhoun, V. D., Clinton,
N., Desrivieres, S., … Westlye, L. (2023). Addressing global environmental challenges
to mental health using population neuroscience: A review. JAMA Psychiatry.
American Medical Association. https://doi.org/10.1001/jamapsychiatry.2023.2996'
chicago: 'Schumann, Gunter, Ole A. Andreassen, Tobias Banaschewski, Vince D. Calhoun,
Nicholas Clinton, Sylvane Desrivieres, Ragnhild Eek Brandlistuen, et al. “Addressing
Global Environmental Challenges to Mental Health Using Population Neuroscience:
A Review.” JAMA Psychiatry. American Medical Association, 2023. https://doi.org/10.1001/jamapsychiatry.2023.2996.'
ieee: 'G. Schumann et al., “Addressing global environmental challenges to
mental health using population neuroscience: A review,” JAMA Psychiatry,
vol. 80, no. 10. American Medical Association, pp. 1066–1074, 2023.'
ista: 'Schumann G, Andreassen OA, Banaschewski T, Calhoun VD, Clinton N, Desrivieres
S, Brandlistuen RE, Feng J, Hese S, Hitchen E, Hoffmann P, Jia T, Jirsa V, Marquand
AF, Nees F, Nöthen MM, Novarino G, Polemiti E, Ralser M, Rapp M, Schepanski K,
Schikowski T, Slater M, Sommer P, Stahl BC, Thompson PM, Twardziok S, Van Der
Meer D, Walter H, Westlye L. 2023. Addressing global environmental challenges
to mental health using population neuroscience: A review. JAMA Psychiatry. 80(10),
1066–1074.'
mla: 'Schumann, Gunter, et al. “Addressing Global Environmental Challenges to Mental
Health Using Population Neuroscience: A Review.” JAMA Psychiatry, vol.
80, no. 10, American Medical Association, 2023, pp. 1066–74, doi:10.1001/jamapsychiatry.2023.2996.'
short: G. Schumann, O.A. Andreassen, T. Banaschewski, V.D. Calhoun, N. Clinton,
S. Desrivieres, R.E. Brandlistuen, J. Feng, S. Hese, E. Hitchen, P. Hoffmann,
T. Jia, V. Jirsa, A.F. Marquand, F. Nees, M.M. Nöthen, G. Novarino, E. Polemiti,
M. Ralser, M. Rapp, K. Schepanski, T. Schikowski, M. Slater, P. Sommer, B.C. Stahl,
P.M. Thompson, S. Twardziok, D. Van Der Meer, H. Walter, L. Westlye, JAMA Psychiatry
80 (2023) 1066–1074.
date_created: 2023-10-22T22:01:14Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-31T12:17:20Z
day: '01'
department:
- _id: GaNo
doi: 10.1001/jamapsychiatry.2023.2996
external_id:
pmid:
- '37610741'
intvolume: ' 80'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1066-1074
pmid: 1
publication: JAMA Psychiatry
publication_identifier:
eissn:
- 2168-6238
publication_status: published
publisher: American Medical Association
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Addressing global environmental challenges to mental health using population
neuroscience: A review'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2023'
...
---
_id: '14441'
abstract:
- lang: eng
text: We study the Fröhlich polaron model in R3, and establish the subleading term
in the strong coupling asymptotics of its ground state energy, corresponding to
the quantum corrections to the classical energy determined by the Pekar approximation.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is acknowledged. Open access funding
provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Brooks M, Seiringer R. The Fröhlich Polaron at strong coupling: Part I - The
quantum correction to the classical energy. Communications in Mathematical
Physics. 2023;404:287-337. doi:10.1007/s00220-023-04841-3'
apa: 'Brooks, M., & Seiringer, R. (2023). The Fröhlich Polaron at strong coupling:
Part I - The quantum correction to the classical energy. Communications in
Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04841-3'
chicago: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong
Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications
in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04841-3.'
ieee: 'M. Brooks and R. Seiringer, “The Fröhlich Polaron at strong coupling: Part
I - The quantum correction to the classical energy,” Communications in Mathematical
Physics, vol. 404. Springer Nature, pp. 287–337, 2023.'
ista: 'Brooks M, Seiringer R. 2023. The Fröhlich Polaron at strong coupling: Part
I - The quantum correction to the classical energy. Communications in Mathematical
Physics. 404, 287–337.'
mla: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling:
Part I - The Quantum Correction to the Classical Energy.” Communications in
Mathematical Physics, vol. 404, Springer Nature, 2023, pp. 287–337, doi:10.1007/s00220-023-04841-3.'
short: M. Brooks, R. Seiringer, Communications in Mathematical Physics 404 (2023)
287–337.
date_created: 2023-10-22T22:01:13Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-10-31T12:22:51Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00220-023-04841-3
ec_funded: 1
external_id:
arxiv:
- '2207.03156'
file:
- access_level: open_access
checksum: 1ae49b39247cb6b40ff75997381581b8
content_type: application/pdf
creator: dernst
date_created: 2023-10-31T12:21:39Z
date_updated: 2023-10-31T12:21:39Z
file_id: '14477'
file_name: 2023_CommMathPhysics_Brooks.pdf
file_size: 832375
relation: main_file
success: 1
file_date_updated: 2023-10-31T12:21:39Z
has_accepted_license: '1'
intvolume: ' 404'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 287-337
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Fröhlich Polaron at strong coupling: Part I - The quantum correction to
the classical energy'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 404
year: '2023'
...
---
_id: '14448'
abstract:
- lang: eng
text: We consider the problem of solving LP relaxations of MAP-MRF inference problems,
and in particular the method proposed recently in [16], [35]. As a key computational
subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth
convex function over a combinatorial polytope. We propose an efficient implementation
of this subroutine based on in-face Frank-Wolfe directions, introduced in [4]
in a different context. More generally, we define an abstract data structure for
a combinatorial subproblem that enables in-face FW directions, and describe its
specialization for tree-structured MAP-MRF inference subproblems. Experimental
results indicate that the resulting method is the current state-of-art LP solver
for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Solving relaxations of MAP-MRF problems: Combinatorial in-face
Frank-Wolfe directions. In: Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition. Vol 2023. IEEE; 2023:11980-11989.
doi:10.1109/CVPR52729.2023.01153'
apa: 'Kolmogorov, V. (2023). Solving relaxations of MAP-MRF problems: Combinatorial
in-face Frank-Wolfe directions. In Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition (Vol. 2023, pp. 11980–11989).
Vancouver, Canada: IEEE. https://doi.org/10.1109/CVPR52729.2023.01153'
chicago: 'Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial
in-Face Frank-Wolfe Directions.” In Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, 2023:11980–89. IEEE,
2023. https://doi.org/10.1109/CVPR52729.2023.01153.'
ieee: 'V. Kolmogorov, “Solving relaxations of MAP-MRF problems: Combinatorial in-face
Frank-Wolfe directions,” in Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, Vancouver, Canada, 2023, vol.
2023, pp. 11980–11989.'
ista: 'Kolmogorov V. 2023. Solving relaxations of MAP-MRF problems: Combinatorial
in-face Frank-Wolfe directions. Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision
and Pattern Recognition vol. 2023, 11980–11989.'
mla: 'Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial
in-Face Frank-Wolfe Directions.” Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, vol. 2023, IEEE, 2023, pp. 11980–89,
doi:10.1109/CVPR52729.2023.01153.'
short: V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on
Computer Vision and Pattern Recognition, IEEE, 2023, pp. 11980–11989.
conference:
end_date: 2023-06-24
location: Vancouver, Canada
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2023-06-17
date_created: 2023-10-22T22:01:16Z
date_published: 2023-08-22T00:00:00Z
date_updated: 2023-10-31T12:01:24Z
day: '22'
department:
- _id: VlKo
doi: 10.1109/CVPR52729.2023.01153
external_id:
arxiv:
- '2010.09567'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2010.09567'
month: '08'
oa: 1
oa_version: Preprint
page: 11980-11989
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- '9798350301298'
issn:
- 1063-6919
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe
directions'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '12672'
abstract:
- lang: eng
text: Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited
over many generations. Such inheritance is thought to be mediated by a semiconservative
mechanism that produces binary present/absent methylation patterns. However, we
show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic
mCG is stably inherited across many generations and is quantitatively associated
with transposon expression. We develop a mathematical model that estimates the
rates of semiconservative maintenance failure and de novo methylation at each
transposon, demonstrating that mCG can be stably inherited at any level via a
dynamic balance of these activities. We find that DRM2 – the core methyltransferase
of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic
de novo mCG, with de novo rates orders of magnitude higher than previously thought,
whereas chromomethylases make smaller contributions. Our results demonstrate that
stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive
de novo methylation.
acknowledgement: The authors would like to thank Jasper Rine for advice and mentorship
to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for
support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with
analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute
Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research
Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from
the Helen Hay Whitney Foundation to D.B.L.
article_number: '112132'
article_processing_charge: Yes
article_type: original
author:
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Jack
full_name: Colicchio, Jack
last_name: Colicchio
- first_name: Ian
full_name: Anderson, Ian
last_name: Anderson
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- 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: Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports.
2023;42(3). doi:10.1016/j.celrep.2023.112132
apa: Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman,
D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG
methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132
chicago: Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey,
Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman.
“Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation
in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
ieee: D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons,” Cell Reports,
vol. 42, no. 3. Elsevier, 2023.
ista: Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng
X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3),
112132.
mla: Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance
of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no.
3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.
short: D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson,
X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).
date_created: 2023-02-23T09:17:44Z
date_published: 2023-03-28T00:00:00Z
date_updated: 2023-11-02T12:23:45Z
day: '28'
ddc:
- '580'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.celrep.2023.112132
ec_funded: 1
external_id:
isi:
- '000944921600001'
file:
- access_level: open_access
checksum: 6cbc44fdb18bf18834c9e2a5b9c67123
content_type: application/pdf
creator: kschuh
date_created: 2023-05-11T10:41:42Z
date_updated: 2023-05-11T10:41:42Z
file_id: '12941'
file_name: 2023_CellReports_Lyons.pdf
file_size: 8401261
relation: main_file
success: 1
file_date_updated: 2023-05-11T10:41:42Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extensive de novo activity stabilizes epigenetic inheritance of CG methylation
in Arabidopsis transposons
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '13178'
abstract:
- lang: eng
text: We consider the large polaron described by the Fröhlich Hamiltonian and study
its energy-momentum relation defined as the lowest possible energy as a function
of the total momentum. Using a suitable family of trial states, we derive an optimal
parabolic upper bound for the energy-momentum relation in the limit of strong
coupling. The upper bound consists of a momentum independent term that agrees
with the predicted two-term expansion for the ground state energy of the strongly
coupled polaron at rest and a term that is quadratic in the momentum with coefficient
given by the inverse of twice the classical effective mass introduced by Landau
and Pekar.
acknowledgement: This research was supported by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation programme grant
agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie grant agreement No. 665386
(K.M.).
article_processing_charge: Yes
article_type: original
author:
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mitrouskas DJ, Mysliwy K, Seiringer R. Optimal parabolic upper bound for the
energy-momentum relation of a strongly coupled polaron. Forum of Mathematics.
2023;11:1-52. doi:10.1017/fms.2023.45
apa: Mitrouskas, D. J., Mysliwy, K., & Seiringer, R. (2023). Optimal parabolic
upper bound for the energy-momentum relation of a strongly coupled polaron. Forum
of Mathematics. Cambridge University Press. https://doi.org/10.1017/fms.2023.45
chicago: Mitrouskas, David Johannes, Krzysztof Mysliwy, and Robert Seiringer. “Optimal
Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.”
Forum of Mathematics. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.45.
ieee: D. J. Mitrouskas, K. Mysliwy, and R. Seiringer, “Optimal parabolic upper bound
for the energy-momentum relation of a strongly coupled polaron,” Forum of Mathematics,
vol. 11. Cambridge University Press, pp. 1–52, 2023.
ista: Mitrouskas DJ, Mysliwy K, Seiringer R. 2023. Optimal parabolic upper bound
for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics.
11, 1–52.
mla: Mitrouskas, David Johannes, et al. “Optimal Parabolic Upper Bound for the Energy-Momentum
Relation of a Strongly Coupled Polaron.” Forum of Mathematics, vol. 11,
Cambridge University Press, 2023, pp. 1–52, doi:10.1017/fms.2023.45.
short: D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023)
1–52.
date_created: 2023-07-02T22:00:43Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2023-11-02T12:30:50Z
day: '13'
ddc:
- '500'
department:
- _id: RoSe
doi: 10.1017/fms.2023.45
ec_funded: 1
external_id:
arxiv:
- '2203.02454'
isi:
- '001005008800001'
file:
- access_level: open_access
checksum: f672eb7dd015c472c9a04f1b9bf9df7d
content_type: application/pdf
creator: alisjak
date_created: 2023-07-03T10:36:25Z
date_updated: 2023-07-03T10:36:25Z
file_id: '13186'
file_name: 2023_ForumofMathematics.Sigma_Mitrouskas.pdf
file_size: 943192
relation: main_file
success: 1
file_date_updated: 2023-07-03T10:36:25Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-52
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Forum of Mathematics
publication_identifier:
eissn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal parabolic upper bound for the energy-momentum relation of a strongly
coupled polaron
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14484'
abstract:
- lang: eng
text: Intercellular signaling molecules, known as morphogens, act at a long range
in developing tissues to provide spatial information and control properties such
as cell fate and tissue growth. The production, transport, and removal of morphogens
shape their concentration profiles in time and space. Downstream signaling cascades
and gene regulatory networks within cells then convert the spatiotemporal morphogen
profiles into distinct cellular responses. Current challenges are to understand
the diverse molecular and cellular mechanisms underlying morphogen gradient formation,
as well as the logic of downstream regulatory circuits involved in morphogen interpretation.
This knowledge, combining experimental and theoretical results, is essential to
understand emerging properties of morphogen-controlled systems, such as robustness
and scaling.
acknowledgement: We are grateful to Zena Hadjivasiliou for comments on this article.
A.K. is supported by grants from the European Research Council under the European
Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe
(101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is
supported by the Francis Crick Institute, which receives its core funding from Cancer
Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome
Trust (CC001051), and by a grant from the European Research Council under the EU
Horizon 2020 research and innovation program (742138).
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
citation:
ama: Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual
Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522
apa: Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens.
Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522
chicago: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.”
Annual Review of Cell and Developmental Biology. Annual Reviews, 2023.
https://doi.org/10.1146/annurev-cellbio-020823-011522.
ieee: A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,”
Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews,
pp. 91–121, 2023.
ista: Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual
Review of Cell and Developmental Biology. 39, 91–121.
mla: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.”
Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews,
2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522.
short: A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39
(2023) 91–121.
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-16T00:00:00Z
date_updated: 2023-11-06T09:56:24Z
day: '16'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1146/annurev-cellbio-020823-011522
ec_funded: 1
external_id:
pmid:
- '37418774'
file:
- access_level: open_access
checksum: 461726014cf5907010afbd418d3c13ec
content_type: application/pdf
creator: dernst
date_created: 2023-11-06T09:47:50Z
date_updated: 2023-11-06T09:47:50Z
file_id: '14491'
file_name: 2023_AnnualReviews_Kicheva.pdf
file_size: 434819
relation: main_file
success: 1
file_date_updated: 2023-11-06T09:47:50Z
has_accepted_license: '1'
intvolume: ' 39'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 91-121
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F07802
name: Morphogen control of growth and pattern in the spinal cord
publication: Annual Review of Cell and Developmental Biology
publication_identifier:
eissn:
- 1530-8995
issn:
- 1081-0706
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of tissue development by morphogens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '14488'
abstract:
- lang: eng
text: 'Portrait viewpoint and illumination editing is an important problem with
several applications in VR/AR, movies, and photography. Comprehensive knowledge
of geometry and illumination is critical for obtaining photorealistic results.
Current methods are unable to explicitly model in 3D while handling both viewpoint
and illumination editing from a single image. In this paper, we propose VoRF,
a novel approach that can take even a single portrait image as input and relight
human heads under novel illuminations that can be viewed from arbitrary viewpoints.
VoRF represents a human head as a continuous volumetric field and learns a prior
model of human heads using a coordinate-based MLP with individual latent spaces
for identity and illumination. The prior model is learned in an auto-decoder manner
over a diverse class of head shapes and appearances, allowing VoRF to generalize
to novel test identities from a single input image. Additionally, VoRF has a reflectance
MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time
(OLAT) images under novel views. We synthesize novel illuminations by combining
these OLAT images with target environment maps. Qualitative and quantitative evaluations
demonstrate the effectiveness of VoRF for relighting and novel view synthesis,
even when applied to unseen subjects under uncontrolled illumination. This work
is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide
extensive evaluation and ablative studies of our model and also provide an application,
where any face can be relighted using textual input.'
acknowledgement: Open Access funding enabled and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Pramod
full_name: Rao, Pramod
last_name: Rao
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Gereon
full_name: Fox, Gereon
last_name: Fox
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Fangneng
full_name: Zhan, Fangneng
last_name: Zhan
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
citation:
ama: Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable
faces. International Journal of Computer Vision. 2023. doi:10.1007/s11263-023-01899-3
apa: Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H.,
… Elgharib, M. (2023). A deeper analysis of volumetric relightiable faces. International
Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3
chicago: Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel,
Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable
Faces.” International Journal of Computer Vision. Springer Nature, 2023.
https://doi.org/10.1007/s11263-023-01899-3.
ieee: P. Rao et al., “A deeper analysis of volumetric relightiable faces,”
International Journal of Computer Vision. Springer Nature, 2023.
ista: Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan
F, Tewari A, Theobalt C, Elgharib M. 2023. A deeper analysis of volumetric relightiable
faces. International Journal of Computer Vision.
mla: Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International
Journal of Computer Vision, Springer Nature, 2023, doi:10.1007/s11263-023-01899-3.
short: P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik,
F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer
Vision (2023).
date_created: 2023-11-05T23:00:54Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-06T08:52:30Z
day: '31'
department:
- _id: BeBi
doi: 10.1007/s11263-023-01899-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s11263-023-01899-3
month: '10'
oa: 1
oa_version: Published Version
publication: International Journal of Computer Vision
publication_identifier:
eissn:
- 1573-1405
issn:
- 0920-5691
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A deeper analysis of volumetric relightiable faces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14487'
abstract:
- lang: eng
text: High Mountain Asia (HMA) is among the most vulnerable water towers globally
and yet future projections of water availability in and from its high-mountain
catchments remain uncertain, as their hydrologic response to ongoing environmental
changes is complex. Mechanistic modeling approaches incorporating cryospheric,
hydrological, and vegetation processes in high spatial, temporal, and physical
detail have never been applied for high-elevation catchments of HMA. We use a
land surface model at high spatial and temporal resolution (100 m and hourly)
to simulate the coupled dynamics of energy, water, and vegetation for the 350
km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological
year against a large set of observations to gain insight into the partitioning
of the water balance at the subseasonal scale and across elevation bands. During
the simulated hydrological year, we find that evapotranspiration is a key component
of the total water balance, as it causes about the equivalent of 20% of all the
available precipitation or 154% of the water production from glacier melt in the
basin to return directly to the atmosphere. The depletion of the cryospheric water
budget is dominated by snow melt, but at high elevations is primarily dictated
by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%)
at the catchment scale, accounting for the equivalent of 11% of snowfall, 17%
of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should
consider sublimation and other evaporative fluxes explicitly, as otherwise water
balance estimates can be ill-quantified.
acknowledgement: This project has received funding from the JSPS-SNSF (Japan Society
for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes
project (HOPE, High-ele-vation precipitation in High Mountain Asia; Grant 183633),
and the European Research Council (ERC) under the European Union's Horizon 2020
research and innovation program (RAVEN, Rapid mass losses of debris-covered glaciers
in High Mountain Asia; Grant 772751). We want to thank in particular T. Gurung,
S. Joshi, J. Shea, W. Immerzeel, and others involved, as well as ICIMOD, for their
efforts over the past years in observing the meteorology of the Langtang catchment,
collecting and organizing the data and making them publicly available. We also thank
the National Geographic Society (Grant NGS-61784R-19) and the Mount Everest Foundation
(reference 19-24) for providing fieldwork funding for C. L. Fyffe. We thank T. Kramer
for help with the WSL Hyperion cluster. We are grate-ful for comments by three anonymous
reviewers and the Associate Editor, who greatly helped to improve the manuscript
further. Open access funding provided by ETH-Bereich Forschungsanstalten.
article_number: e2022WR033841
article_processing_charge: Yes (via OA deal)
article_type: original
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
- first_name: Evan S.
full_name: Miles, Evan S.
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. Land surface modeling in the Himalayas:
On the importance of evaporative fluxes for the water balance of a high-elevation
catchment. Water Resources Research. 2023;59(10). doi:10.1029/2022WR033841'
apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E. S., McCarthy, M., 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. Wiley. https://doi.org/10.1029/2022WR033841'
chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan S. Miles, Michael McCarthy,
Catriona Louise Fyffe, Stefan Fugger, et al. “Land Surface Modeling in the Himalayas:
On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation
Catchment.” Water Resources Research. Wiley, 2023. https://doi.org/10.1029/2022WR033841.'
ieee: 'P. Buri et al., “Land surface modeling in the Himalayas: On the importance
of evaporative fluxes for the water balance of a high-elevation catchment,” Water
Resources Research, vol. 59, no. 10. Wiley, 2023.'
ista: 'Buri P, Fatichi S, Shaw T, Miles ES, McCarthy M, Fyffe CL, Fugger S, Ren
S, Kneib M, Jouberton A, Steiner J, Fujita K, 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.'
mla: 'Buri, Pascal, et al. “Land Surface Modeling in the Himalayas: On the Importance
of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water
Resources Research, vol. 59, no. 10, e2022WR033841, Wiley, 2023, doi:10.1029/2022WR033841.'
short: P. Buri, S. Fatichi, T. Shaw, E.S. Miles, M. McCarthy, C.L. Fyffe, S. Fugger,
S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, Water
Resources Research 59 (2023).
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2023-11-07T08:12:34Z
day: '25'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1029/2022WR033841
file:
- access_level: open_access
checksum: 7ba9c87228dc09029b16bc800a0ef1a1
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T08:10:44Z
date_updated: 2023-11-07T08:10:44Z
file_id: '14495'
file_name: 2023_WaterResourcesResearch_Buri.pdf
file_size: 5554901
relation: main_file
success: 1
file_date_updated: 2023-11-07T08:10:44Z
has_accepted_license: '1'
intvolume: ' 59'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '14494'
relation: research_data
status: public
scopus_import: '1'
status: public
title: '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_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2023'
...
---
_id: '14485'
abstract:
- lang: eng
text: "Batching is a technique that stores multiple keys/values in each node of
a data structure. In sequential search data structures, batching reduces latency
by reducing the number of cache misses and shortening the chain of pointers to
dereference. Applying batching to concurrent data structures is challenging, because
it is difficult to maintain the search property and keep contention low in the
presence of batching.\r\nIn this paper, we present a general methodology for leveraging
batching in concurrent search data structures, called BatchBoost. BatchBoost builds
a search data structure from distinct \"data\" and \"index\" layers. The data
layer’s purpose is to store a batch of key/value pairs in each of its nodes. The
index layer uses an unmodified concurrent search data structure to route operations
to a position in the data layer that is \"close\" to where the corresponding key
should exist. The requirements on the index and data layers are low: with minimal
effort, we were able to compose three highly scalable concurrent search data structures
based on three original data structures as the index layers with a batched version
of the Lazy List as the data layer. The resulting BatchBoost data structures provide
significant performance improvements over their original counterparts."
alternative_title:
- LIPIcs
article_number: '35'
article_processing_charge: Yes
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- first_name: Michael
full_name: Anoprenko, Michael
last_name: Anoprenko
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Michael
full_name: Spear, Michael
last_name: Spear
citation:
ama: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost:
Universal batching for concurrent data structures. In: 37th International Symposium
on Distributed Computing. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.DISC.2023.35'
apa: 'Aksenov, V., Anoprenko, M., Fedorov, A., & Spear, M. (2023). Brief announcement:
BatchBoost: Universal batching for concurrent data structures. In 37th International
Symposium on Distributed Computing (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2023.35'
chicago: 'Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear.
“Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.”
In 37th International Symposium on Distributed Computing, Vol. 281. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.DISC.2023.35.'
ieee: 'V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement:
BatchBoost: Universal batching for concurrent data structures,” in 37th International
Symposium on Distributed Computing, L’Aquila, Italy, 2023, vol. 281.'
ista: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost:
Universal batching for concurrent data structures. 37th International Symposium
on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol.
281, 35.'
mla: 'Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching
for Concurrent Data Structures.” 37th International Symposium on Distributed
Computing, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.DISC.2023.35.'
short: V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium
on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-10-13
location: L'Aquila, Italy
name: 'DISC: Symposium on Distributed Computing'
start_date: 2023-10-09
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-07T07:48:01Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
doi: 10.4230/LIPIcs.DISC.2023.35
file:
- access_level: open_access
checksum: d9f8d2915cccdf2df5905b7cd1b4a560
content_type: application/pdf
creator: dernst
date_created: 2023-11-06T11:45:21Z
date_updated: 2023-11-06T11:45:21Z
file_id: '14492'
file_name: 2023_LIPIcs_Aksenov.pdf
file_size: 646665
relation: main_file
success: 1
file_date_updated: 2023-11-06T11:45:21Z
has_accepted_license: '1'
intvolume: ' 281'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: 37th International Symposium on Distributed Computing
publication_identifier:
isbn:
- '9783959773010'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: BatchBoost: Universal batching for concurrent data structures'
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: 281
year: '2023'
...
---
_id: '14486'
abstract:
- lang: eng
text: We present a minimal model of ferroelectric large polarons, which are suggested
as one of the mechanisms responsible for the unique charge transport properties
of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions
lead to long-range ferroelectric ordering of rotors, which strongly affects the
carrier mobility. In the nonperturbative regime, where our theory cannot be reduced
to any of the earlier models, we reveal that the polaron is characterized by large
coherence length and a roughly tenfold increase of the effective mass as compared
to the bare mass. These results are in good agreement with other theoretical predictions
for ferroelectric polarons. Our model establishes a general phenomenological framework
for ferroelectric polarons providing the starting point for future studies of
their role in the transport properties of hybrid organic-inorganic perovskites.
acknowledgement: We thank Zh. Alpichshev, A. Volosniev, and A. V. Zampetaki for fruitful
discussions and comments. This project received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 101034413. M.L. acknowledges support by the European Research
Council (ERC) Starting Grant No. 801770 (ANGULON).
article_number: '043016'
article_processing_charge: Yes
article_type: original
author:
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Koutentakis G, Ghazaryan A, Lemeshko M. Rotor lattice model of ferroelectric
large polarons. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043016
apa: Koutentakis, G., Ghazaryan, A., & Lemeshko, M. (2023). Rotor lattice model
of ferroelectric large polarons. Physical Review Research. American Physical
Society. https://doi.org/10.1103/PhysRevResearch.5.043016
chicago: Koutentakis, Georgios, Areg Ghazaryan, and Mikhail Lemeshko. “Rotor Lattice
Model of Ferroelectric Large Polarons.” Physical Review Research. American
Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043016.
ieee: G. Koutentakis, A. Ghazaryan, and M. Lemeshko, “Rotor lattice model of ferroelectric
large polarons,” Physical Review Research, vol. 5, no. 4. American Physical
Society, 2023.
ista: Koutentakis G, Ghazaryan A, Lemeshko M. 2023. Rotor lattice model of ferroelectric
large polarons. Physical Review Research. 5(4), 043016.
mla: Koutentakis, Georgios, et al. “Rotor Lattice Model of Ferroelectric Large Polarons.”
Physical Review Research, vol. 5, no. 4, 043016, American Physical Society,
2023, doi:10.1103/PhysRevResearch.5.043016.
short: G. Koutentakis, A. Ghazaryan, M. Lemeshko, Physical Review Research 5 (2023).
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-05T00:00:00Z
date_updated: 2023-11-07T07:53:39Z
day: '05'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.5.043016
ec_funded: 1
external_id:
arxiv:
- '2301.09875'
file:
- access_level: open_access
checksum: cb8de8fed6e09df1a18bd5a5aec5c55c
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T07:52:46Z
date_updated: 2023-11-07T07:52:46Z
file_id: '14493'
file_name: 2023_PhysReviewResearch_Koutentakis.pdf
file_size: 1127522
relation: main_file
success: 1
file_date_updated: 2023-11-07T07:52:46Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rotor lattice model of ferroelectric large polarons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14313'
abstract:
- lang: eng
text: To respond to auxin, the chief orchestrator of their multicellularity, plants
evolved multiple receptor systems and signal transduction cascades. Despite decades
of research, however, we are still lacking a satisfactory synthesis of various
auxin signaling mechanisms. The chief discrepancy and historical controversy of
the field is that of rapid and slow auxin effects on plant physiology and development.
How is it possible that ions begin to trickle across the plasma membrane as soon
as auxin enters the cell, even though the best-characterized transcriptional auxin
pathway can take effect only after tens of minutes? Recently, unexpected progress
has been made in understanding this and other unknowns of auxin signaling. We
provide a perspective on these exciting developments and concepts whose general
applicability might have ramifications beyond auxin signaling.
acknowledgement: The opening quote is not intended to reflect any political views
of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld
or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote
led to both public and academic debates on the concept of known and unknown unknowns,
which can be applied to the recent unexpected developments in the auxin signaling
field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation
and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain
for discussion of Greek mythology.
article_number: '102443'
article_processing_charge: No
article_type: review
author:
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443'
apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and
new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443'
chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and
New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.'
ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current
Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.'
ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 75(10), 102443.'
mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.”
Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023,
doi:10.1016/j.pbi.2023.102443.'
short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-07T08:17:13Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2023.102443
external_id:
pmid:
- '37666097'
file:
- access_level: open_access
checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:03:20Z
date_updated: 2023-11-02T17:03:20Z
file_id: '14482'
file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf
file_size: 737872
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:03:20Z
has_accepted_license: '1'
intvolume: ' 75'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rapid auxin signaling: Unknowns old and new'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2023'
...
---
_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
- 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: 2023-11-07T08:12:35Z
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
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).
date_created: 2023-11-07T09:02:48Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2023-11-07T09:18:57Z
day: '24'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1017/fmp.2023.17
external_id:
arxiv:
- '2208.02874'
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'
keyword:
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Mathematical Physics
- Statistics and Probability
- Algebra and Number Theory
- Analysis
language:
- iso: eng
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14281'
abstract:
- lang: eng
text: In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to
how transistors control information flow in computing devices. Designing proteins
with two distinct but fully structured conformations is a challenge for protein
design as it requires sculpting an energy landscape with two distinct minima.
Here we describe the design of “hinge” proteins that populate one designed state
in the absence of ligand and a second designed state in the presence of ligand.
X-ray crystallography, electron microscopy, double electron-electron resonance
spectroscopy, and binding measurements demonstrate that despite the significant
structural differences the two states are designed with atomic level accuracy
and that the conformational and binding equilibria are closely coupled.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Philip J. Y.
full_name: Leung, Philip J. Y.
last_name: Leung
- first_name: Maxx H.
full_name: Tessmer, Maxx H.
last_name: Tessmer
- first_name: Adam
full_name: Broerman, Adam
last_name: Broerman
- first_name: Cullen
full_name: Demakis, Cullen
last_name: Demakis
- first_name: Acacia F.
full_name: Dishman, Acacia F.
last_name: Dishman
- first_name: Arvind
full_name: Pillai, Arvind
last_name: Pillai
- first_name: Abbas
full_name: Idris, Abbas
last_name: Idris
- first_name: David
full_name: Juergens, David
last_name: Juergens
- first_name: Justas
full_name: Dauparas, Justas
last_name: Dauparas
- first_name: Xinting
full_name: Li, Xinting
last_name: Li
- first_name: Paul M.
full_name: Levine, Paul M.
last_name: Levine
- first_name: Mila
full_name: Lamb, Mila
last_name: Lamb
- first_name: Ryanne K.
full_name: Ballard, Ryanne K.
last_name: Ballard
- first_name: Stacey R.
full_name: Gerben, Stacey R.
last_name: Gerben
- first_name: Hannah
full_name: Nguyen, Hannah
last_name: Nguyen
- first_name: Alex
full_name: Kang, Alex
last_name: Kang
- first_name: Banumathi
full_name: Sankaran, Banumathi
last_name: Sankaran
- first_name: Asim K.
full_name: Bera, Asim K.
last_name: Bera
- first_name: Brian F.
full_name: Volkman, Brian F.
last_name: Volkman
- first_name: Jeff
full_name: Nivala, Jeff
last_name: Nivala
- first_name: Stefan
full_name: Stoll, Stefan
last_name: Stoll
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive
two-state hinge proteins. Science. 2023;381(6659):754-760. doi:10.1126/science.adg7731
apa: Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis,
C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state
hinge proteins. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adg7731
chicago: Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman,
Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive
Two-State Hinge Proteins.” Science. American Association for the Advancement
of Science, 2023. https://doi.org/10.1126/science.adg7731.
ieee: F. M. Praetorius et al., “Design of stimulus-responsive two-state hinge
proteins,” Science, vol. 381, no. 6659. American Association for the Advancement
of Science, pp. 754–760, 2023.
ista: Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai
A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben
SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker
D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659),
754–760.
mla: Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge
Proteins.” Science, vol. 381, no. 6659, American Association for the Advancement
of Science, 2023, pp. 754–60, doi:10.1126/science.adg7731.
short: F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F.
Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M.
Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F.
Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.
date_created: 2023-09-06T12:04:23Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2023-11-07T12:42:09Z
day: '17'
doi: 10.1126/science.adg7731
extern: '1'
external_id:
pmid:
- '37590357'
intvolume: ' 381'
issue: '6659'
language:
- iso: eng
month: '08'
oa_version: None
page: 754-760
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design of stimulus-responsive two-state hinge proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '14294'
abstract:
- lang: eng
text: Growth factors and cytokines signal by binding to the extracellular domains
of their receptors and drive association and transphosphorylation of the receptor
intracellular tyrosine kinase domains, initiating downstream signaling cascades.
To enable systematic exploration of how receptor valency and geometry affects
signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using
repeat protein building blocks that can be modularly extended. By incorporating
a de novo designed fibroblast growth-factor receptor (FGFR) binding module into
these scaffolds, we generated a series of synthetic signaling ligands that exhibit
potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation.
The high specificity of the designed agonists reveal distinct roles for two FGFR
splice variants in driving endothelial and mesenchymal cell fates during early
vascular development. The ability to incorporate receptor binding domains and
repeat extensions in a modular fashion makes our designed scaffolds broadly useful
for probing and manipulating cellular signaling pathways.
article_processing_charge: No
author:
- first_name: Natasha I
full_name: Edman, Natasha I
last_name: Edman
- first_name: Rachel L
full_name: Redler, Rachel L
last_name: Redler
- first_name: Ashish
full_name: Phal, Ashish
last_name: Phal
- first_name: Thomas
full_name: Schlichthaerle, Thomas
last_name: Schlichthaerle
- first_name: Sanjay R
full_name: Srivatsan, Sanjay R
last_name: Srivatsan
- first_name: Ali
full_name: Etemadi, Ali
last_name: Etemadi
- first_name: Seong
full_name: An, Seong
last_name: An
- first_name: Andrew
full_name: Favor, Andrew
last_name: Favor
- first_name: Devon
full_name: Ehnes, Devon
last_name: Ehnes
- first_name: Zhe
full_name: Li, Zhe
last_name: Li
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Max
full_name: Gordon, Max
last_name: Gordon
- first_name: Wei
full_name: Yang, Wei
last_name: Yang
- first_name: Brian
full_name: Coventry, Brian
last_name: Coventry
- first_name: Derrick R
full_name: Hicks, Derrick R
last_name: Hicks
- first_name: Longxing
full_name: Cao, Longxing
last_name: Cao
- first_name: Neville
full_name: Bethel, Neville
last_name: Bethel
- first_name: Piper
full_name: Heine, Piper
last_name: Heine
- first_name: Analisa N
full_name: Murray, Analisa N
last_name: Murray
- first_name: Stacey
full_name: Gerben, Stacey
last_name: Gerben
- first_name: Lauren
full_name: Carter, Lauren
last_name: Carter
- first_name: Marcos
full_name: Miranda, Marcos
last_name: Miranda
- first_name: Babak
full_name: Negahdari, Babak
last_name: Negahdari
- first_name: Sangwon
full_name: Lee, Sangwon
last_name: Lee
- first_name: Cole
full_name: Trapnell, Cole
last_name: Trapnell
- first_name: Lance
full_name: Stewart, Lance
last_name: Stewart
- first_name: Damian C
full_name: Ekiert, Damian C
last_name: Ekiert
- first_name: Joseph
full_name: Schlessinger, Joseph
last_name: Schlessinger
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Gira
full_name: Bhabha, Gira
last_name: Bhabha
- first_name: Hannele
full_name: Ruohola-Baker, Hannele
last_name: Ruohola-Baker
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and
vascular differentiation using designed oligomeric assemblies. bioRxiv.
doi:10.1101/2023.03.14.532666
apa: Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R.,
Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666
chicago: Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle,
Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling
and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv,
n.d. https://doi.org/10.1101/2023.03.14.532666.
ieee: N. I. Edman et al., “Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies,” bioRxiv. .
ista: Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An
S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks
DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari
B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha
G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666.
mla: Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular
Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666.
short: N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi,
S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry,
D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M.
Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger,
J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).
date_created: 2023-09-06T12:31:49Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-11-07T12:21:58Z
day: '15'
doi: 10.1101/2023.03.14.532666
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.14.532666
month: '03'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Modulation of FGF pathway signaling and vascular differentiation using designed
oligomeric assemblies
type: preprint
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
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: 2023-11-13T08:01:57Z
day: '29'
department:
- _id: MiLe
doi: 10.1016/j.physrep.2023.10.004
ec_funded: 1
external_id:
arxiv:
- '2202.11071'
intvolume: ' 1042'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1042
year: '2023'
...
---
_id: '12869'
abstract:
- lang: eng
text: 'We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately round cultures get a competitive advantage. We first analyse the
model with periodic boundary conditions, where we study how the model can end
up in a fixed state, i.e. freezes. Then we implement the model on the European
geography with mountains and rivers. We see how the model reproduces some qualitative
features of European culture formation, namely that rivers and mountains are more
frequently borders between cultures, mountainous regions tend to have higher cultural
diversity and the central European plain has less clear cultural borders. '
acknowledgement: 'FRK acknowledges support from the Villum Foundation for support
through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator
(Grant No. 25452) programs. '
article_processing_charge: No
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton
model of culture formation. 2023. doi:10.15479/AT:ISTA:12869'
apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic
cellular automaton model of culture formation. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:12869'
chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data
for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.'
ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular
automaton model of culture formation.” Institute of Science and Technology Austria,
2023.'
ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular
automaton model of culture formation, Institute of Science and Technology Austria,
10.15479/AT:ISTA:12869.'
mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for:
A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.'
short: F.R. Klausen, A.B. Lauritsen, (2023).
date_created: 2023-04-26T12:34:49Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-11-13T07:47:29Z
day: '26'
ddc:
- '000'
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/AT:ISTA:12869
file:
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checksum: 85ede12d38bb8d944022a8cba4d719f5
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creator: alaurits
date_created: 2023-04-26T12:30:06Z
date_updated: 2023-04-26T12:30:06Z
file_id: '12870'
file_name: README.md
file_size: 4567
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success: 1
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date_created: 2023-04-26T12:27:34Z
date_updated: 2023-04-26T12:27:34Z
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file_name: simulations_era=10_flux_varied_europe.zip
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date_updated: 2023-04-26T12:29:53Z
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file_size: 1743893150
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oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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- id: '14505'
relation: used_in_publication
status: for_moderation
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relation: used_in_publication
status: public
status: public
title: 'Research data for: A stochastic cellular automaton model of culture formation'
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12890'
abstract:
- lang: eng
text: We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately geometrically round cultures get a competitive advantage. We first
analyze the model with periodic boundary conditions, where we study how the model
can end up in a fixed state, i.e., freezes. Then we implement the model on the
European geography with mountains and rivers. We see how the model reproduces
some qualitative features of European culture formation, namely, that rivers and
mountains are more frequently borders between cultures, mountainous regions tend
to have higher cultural diversity, and the central European plain has less clear
cultural borders.
acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen
and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support
from the Villum Foundation for support through the QMATH center of Excellence (Grant
No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.
article_number: '054307'
article_processing_charge: No
article_type: original
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation.
Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307
apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton
model of culture formation. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.108.054307
chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.
ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of
culture formation,” Physical Review E, vol. 108, no. 5. American Physical
Society, 2023.
ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture
formation. Physical Review E. 108(5), 054307.
mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E, vol. 108, no.
5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.
short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).
date_created: 2023-05-04T08:35:01Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-13T07:47:30Z
day: '08'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1103/PhysRevE.108.054307
external_id:
arxiv:
- '2305.02153'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.02153
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/FrederikRavnKlausen/model-for-culture-formation
record:
- id: '12869'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Stochastic cellular automaton model of culture formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
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
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-13T08:52:01Z
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: '14517'
abstract:
- lang: eng
text: 'State-of-the-art transmon qubits rely on large capacitors, which systematically
improve their coherence due to reduced surface-loss participation. However, this
approach increases both the footprint and the parasitic cross-coupling and is
ultimately limited by radiation losses—a potential roadblock for scaling up quantum
processors to millions of qubits. In this work we present transmon qubits with
sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined
from commercial silicon-on-insulator wafers and shadow evaporated with aluminum.
We achieve a vacuum participation ratio up to 99.6% in an in-plane design that
is compatible with standard coplanar circuits. Qubit relaxationtime measurements
for small gaps with high zero-point electric field variance of up to 22 V/m reveal
a double exponential decay indicating comparably strong qubit interaction with
long-lived two-level systems. The exceptionally high selectivity of up to 20 dB
to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon
dielectric loss tangent of aluminum oxide previously exposed to ambient conditions.
In terms of future scaling potential, we achieve a ratio of qubit quality factor
to a footprint area equal to 20 µm−2, which is comparable with the highest T1
devices relying on larger geometries, a value that could improve substantially
for lower surface-loss superconductors. '
acknowledged_ssus:
- _id: NanoFab
acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through
BeyondC (F7105), the European Research Council under Grant Agreement No. 758053
(ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient
of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences,
and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from
Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges
support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project
No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility."
article_number: '044054'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits:
Selective and sensitive probes for superconductor surface losses. Physical
Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054'
apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh,
S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and
sensitive probes for superconductor surface losses. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054'
chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea
Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits:
Selective and Sensitive Probes for Superconductor Surface Losses.” Physical
Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.'
ieee: 'M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective
and sensitive probes for superconductor surface losses,” Physical Review Applied,
vol. 20, no. 4. American Physical Society, 2023.'
ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink
JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for
superconductor surface losses. Physical Review Applied. 20(4), 044054.'
mla: 'Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and
Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied,
vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.'
short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh,
J.M. Fink, Physical Review Applied 20 (2023).
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2023-11-13T09:22:47Z
day: '20'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.20.044054
ec_funded: 1
external_id:
arxiv:
- '2206.14104'
intvolume: ' 20'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.14104
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
- _id: bdb7cfc1-d553-11ed-ba76-d2eaab167738
grant_number: '101080139'
name: Open Superconducting Quantum Computers (OpenSuperQPlus)
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14520'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor
surface losses'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
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
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: 2023-11-13T09:03:30Z
day: '26'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevX.13.041017
external_id:
arxiv:
- '2203.03461'
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
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: 2023-11-13T09:21:30Z
day: '20'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevLett.131.168201
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'
issue: '16'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
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: 2023-11-13T09:21:31Z
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: '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
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
date_created: 2023-11-12T23:00:56Z
date_published: 2023-09-28T00:00:00Z
date_updated: 2023-11-13T10:18:45Z
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: '13096'
abstract:
- lang: eng
text: Eukaryotic cells can undergo different forms of programmed cell death, many
of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7.
Plasma membrane rupture was long thought to be driven by osmotic pressure, but
it has recently been shown to be in many cases an active process, mediated by
the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the
mechanism by which it ruptures membranes. Super-resolution microscopy reveals
that NINJ1 clusters into structurally diverse assemblies in the membranes of dying
cells, in particular large, filamentous assemblies with branched morphology. A
cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like
array of transmembrane α-helices. Filament directionality and stability is defined
by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1
filament features a hydrophilic side and a hydrophobic side, and molecular dynamics
simulations show that it can stably cap membrane edges. The function of the resulting
supramolecular arrangement was validated by site-directed mutagenesis. Our data
thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1
insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic
filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore
an interactive component of the eukaryotic cell membrane that functions as an
in-built breaking point in response to activation of cell death.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft under
Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation
Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project
funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute
and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H.
and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz
Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship
funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H.
and by the Scientific Service Units of IST Austria through resources provided by
the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were
performed on the HoreKa supercomputer funded by the Ministry of Science, Research
and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research.
The authors thank the BioEM Lab of the Biozentrum, University of Basel for support;
V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt
for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P.
Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und
M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created
with BioRender.com.\r\nOpen access funding provided by University of Basel."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Morris
full_name: Degen, Morris
last_name: Degen
- first_name: José Carlos
full_name: Santos, José Carlos
last_name: Santos
- first_name: Kristyna
full_name: Pluhackova, Kristyna
last_name: Pluhackova
- first_name: Gonzalo
full_name: Cebrero, Gonzalo
last_name: Cebrero
- first_name: Saray
full_name: Ramos, Saray
last_name: Ramos
- first_name: Gytis
full_name: Jankevicius, Gytis
last_name: Jankevicius
- first_name: Ella
full_name: Hartenian, Ella
last_name: Hartenian
- first_name: Undina
full_name: Guillerm, Undina
id: bb74f472-ae54-11eb-9835-bc9c22fb1183
last_name: Guillerm
- first_name: Stefania A.
full_name: Mari, Stefania A.
last_name: Mari
- first_name: Bastian
full_name: Kohl, Bastian
last_name: Kohl
- first_name: Daniel J.
full_name: Müller, Daniel J.
last_name: Müller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Timm
full_name: Maier, Timm
last_name: Maier
- first_name: Camilo
full_name: Perez, Camilo
last_name: Perez
- first_name: Christian
full_name: Sieben, Christian
last_name: Sieben
- first_name: Petr
full_name: Broz, Petr
last_name: Broz
- first_name: Sebastian
full_name: Hiller, Sebastian
last_name: Hiller
citation:
ama: Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated
plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z
apa: Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius,
G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture
in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z
chicago: Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero,
Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated
Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023.
https://doi.org/10.1038/s41586-023-05991-z.
ieee: M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane
rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071,
2023.
ista: Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian
E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben
C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane
rupture in cell death. Nature. 618, 1065–1071.
mla: Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture
in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.
short: M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius,
E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier,
C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.
date_created: 2023-05-28T22:01:04Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-11-14T11:49:21Z
day: '29'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1038/s41586-023-05991-z
external_id:
isi:
- '000991386800011'
file:
- access_level: open_access
checksum: 0fab69252453bff1de7f0e2eceb76d34
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:48:18Z
date_updated: 2023-11-14T11:48:18Z
file_id: '14533'
file_name: 2023_Nature_Degen.pdf
file_size: 12292188
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:48:18Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1065-1071
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 618
year: '2023'
...
---
_id: '13041'
abstract:
- lang: eng
text: A series of triarylamines was synthesised and screened for their suitability
as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine
was found to be the strongest candidate. Solubility and initial electrochemical
performance were promising; however, polymerisation was observed during electrochemical
cycling leading to rapid capacity fade prescribed to a loss of accessible active
material and the limitation of ion transport processes within the cell. A mixed
electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing
oligomers that consumed less active material reducing rates of degradation in
the redox flow battery. Under these conditions Coulombic efficiency improved by
over 4 %, the maximum number of cycles more than quadrupled and an additional
theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the
first example of triarylamines as catholytes in all-aqueous redox flow batteries
and emphasises the impact supporting electrolytes can have on electrochemical
performance.
acknowledgement: The authors (N.L.F and R.B.J) would like to acknowledge the funding
contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1
and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator
Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge
for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry
service for MS measurements and analysis and Dr Andrew Bond from the University
of Cambridge for XRD measurement and analysis.
article_number: e202300128
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Nadia L.
full_name: Farag, Nadia L.
last_name: Farag
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Alice E.
full_name: Beardmore, Alice E.
last_name: Beardmore
- first_name: Teresa
full_name: Insinna, Teresa
last_name: Insinna
- first_name: Christopher A.
full_name: O'Keefe, Christopher A.
last_name: O'Keefe
- first_name: Peter A.A.
full_name: Klusener, Peter A.A.
last_name: Klusener
- first_name: Clare P.
full_name: Grey, Clare P.
last_name: Grey
- first_name: Dominic S.
full_name: Wright, Dominic S.
last_name: Wright
citation:
ama: Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128
apa: Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A.,
Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous
organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128
chicago: Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher
A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines
as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley,
2023. https://doi.org/10.1002/cssc.202300128.
ieee: N. L. Farag et al., “Triarylamines as catholytes in aqueous organic
redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023.
ista: Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey
CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow
batteries. ChemSusChem. 16(13), e202300128.
mla: Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox
Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023,
doi:10.1002/cssc.202300128.
short: N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A.
Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).
date_created: 2023-05-21T22:01:05Z
date_published: 2023-07-06T00:00:00Z
date_updated: 2023-11-14T11:28:23Z
day: '06'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1002/cssc.202300128
external_id:
isi:
- '000985051300001'
pmid:
- '36970847'
file:
- access_level: open_access
checksum: efa0713289995af83a2147b3e8e1d6a6
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T11:27:16Z
date_updated: 2023-11-14T11:27:16Z
file_id: '14532'
file_name: 2023_ChemSusChem_Farag.pdf
file_size: 1168683
relation: main_file
success: 1
file_date_updated: 2023-11-14T11:27:16Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: ChemSusChem
publication_identifier:
eissn:
- 1864-564X
issn:
- 1864-5631
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Triarylamines as catholytes in aqueous organic redox flow batteries
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
_id: '13118'
abstract:
- lang: eng
text: Under high pressures and temperatures, molecular systems with substantial
polarization charges, such as ammonia and water, are predicted to form superionic
phases and dense fluid states with dissociating molecules and high electrical
conductivity. This behaviour potentially plays a role in explaining the origin
of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought
to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain,
melting curve and electrical conductivity of these superionic phases is therefore
crucial for modelling planetary interiors and dynamos. Here we report the melting
curve of superionic ammonia up to 300 GPa from laser-driven shock compression
of pre-compressed samples and atomistic calculations. We show that ammonia melts
at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical
conductivity exceeds that of water at conditions predicted by hot, super-adiabatic
models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich
dynamo layers.
acknowledgement: We acknowledge the crucial contribution of the LULI2000 laser and
support teams to the success of the experiments. We also thank S. Brygoo and P.
Loubeyre for useful discussions. This research was supported by the French National
Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and
SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and
R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440.
M.B. was supported by the European Union within the Marie Skłodowska-Curie actions
(xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed
at the North-German Supercomputing Alliance facilities.
article_processing_charge: No
article_type: original
author:
- first_name: J.-A.
full_name: Hernandez, J.-A.
last_name: Hernandez
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: S.
full_name: Ninet, S.
last_name: Ninet
- first_name: M.
full_name: French, M.
last_name: French
- first_name: A.
full_name: Benuzzi-Mounaix, A.
last_name: Benuzzi-Mounaix
- first_name: F.
full_name: Datchi, F.
last_name: Datchi
- first_name: M.
full_name: Guarguaglini, M.
last_name: Guarguaglini
- first_name: F.
full_name: Lefevre, F.
last_name: Lefevre
- first_name: F.
full_name: Occelli, F.
last_name: Occelli
- first_name: R.
full_name: Redmer, R.
last_name: Redmer
- first_name: T.
full_name: Vinci, T.
last_name: Vinci
- first_name: A.
full_name: Ravasio, A.
last_name: Ravasio
citation:
ama: Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic
ammonia at planetary interior conditions. Nature Physics. 2023;19:1280-1285.
doi:10.1038/s41567-023-02074-8
apa: Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix,
A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary
interior conditions. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02074-8
chicago: Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02074-8.
ieee: J.-A. Hernandez et al., “Melting curve of superionic ammonia at planetary
interior conditions,” Nature Physics, vol. 19. Springer Nature, pp. 1280–1285,
2023.
ista: Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi
F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting
curve of superionic ammonia at planetary interior conditions. Nature Physics.
19, 1280–1285.
mla: Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary
Interior Conditions.” Nature Physics, vol. 19, Springer Nature, 2023, pp.
1280–85, doi:10.1038/s41567-023-02074-8.
short: J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix,
F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio,
Nature Physics 19 (2023) 1280–1285.
date_created: 2023-06-04T22:01:02Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-14T12:58:31Z
day: '01'
department:
- _id: BiCh
doi: 10.1038/s41567-023-02074-8
external_id:
isi:
- '000996921200001'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1280-1285
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: 10.1038/s41567-023-02130-3
scopus_import: '1'
status: public
title: Melting curve of superionic ammonia at planetary interior conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13119'
abstract:
- lang: eng
text: A density wave (DW) is a fundamental type of long-range order in quantum matter
tied to self-organization into a crystalline structure. The interplay of DW order
with superfluidity can lead to complex scenarios that pose a great challenge to
theoretical analysis. In the past decades, tunable quantum Fermi gases have served
as model systems for exploring the physics of strongly interacting fermions, including
most notably magnetic ordering1, pairing and superfluidity2, and the crossover
from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here,
we realize a Fermi gas featuring both strong, tunable contact interactions and
photon-mediated, spatially structured long-range interactions in a transversely
driven high-finesse optical cavity. Above a critical long-range interaction strength,
DW order is stabilized in the system, which we identify via its superradiant light-scattering
properties. We quantitatively measure the variation of the onset of DW order as
the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid
and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field
theory. The atomic DW susceptibility varies over an order of magnitude upon tuning
the strength and the sign of the long-range interactions below the self-ordering
threshold, demonstrating independent and simultaneous control over the contact
and long-range interactions. Therefore, our experimental setup provides a fully
tunable and microscopically controllable platform for the experimental study of
the interplay of superfluidity and DW order.
acknowledgement: Open access funding provided by EPFL Lausanne.We acknowledge discussions
with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance
in the final stages of the experiment. We acknowledge funding from the European
Research Council under the European Union Horizon 2020 Research and Innovation Programme
(Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654).
F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone
Project P 35891-N).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Victor
full_name: Helson, Victor
last_name: Helson
- first_name: Timo
full_name: Zwettler, Timo
last_name: Zwettler
- first_name: Farokh
full_name: Mivehvar, Farokh
last_name: Mivehvar
- first_name: Elvia
full_name: Colella, Elvia
last_name: Colella
- first_name: Kevin Etienne Robert
full_name: Roux, Kevin Etienne Robert
id: 53f93ea2-803f-11ed-ab7e-b283135794ef
last_name: Roux
- first_name: Hideki
full_name: Konishi, Hideki
last_name: Konishi
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Jean Philippe
full_name: Brantut, Jean Philippe
last_name: Brantut
citation:
ama: Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary
Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720.
doi:10.1038/s41586-023-06018-3
apa: Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi,
H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3
chicago: Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne
Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave
Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature.
Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3.
ieee: V. Helson et al., “Density-wave ordering in a unitary Fermi gas with
photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720,
2023.
ista: Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H,
Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated
interactions. Nature. 618, 716–720.
mla: Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated
Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3.
short: V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi,
H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.
date_created: 2023-06-04T22:01:03Z
date_published: 2023-06-22T00:00:00Z
date_updated: 2023-11-14T13:02:50Z
day: '22'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41586-023-06018-3
external_id:
isi:
- '001001139300008'
file:
- access_level: open_access
checksum: 4887a296e3b6f54e8c0b946cbfd24f49
content_type: application/pdf
creator: dernst
date_created: 2023-11-14T13:00:19Z
date_updated: 2023-11-14T13:00:19Z
file_id: '14534'
file_name: 2023_Nature_Helson.pdf
file_size: 8156497
relation: main_file
success: 1
file_date_updated: 2023-11-14T13:00:19Z
has_accepted_license: '1'
intvolume: ' 618'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 716-720
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Density-wave ordering in a unitary Fermi gas with photon-mediated interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 618
year: '2023'
...
---
_id: '12911'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional
composite quantum system at positive temperature as a non-commutative entropy
regularized Optimal Transport problem. We develop a new approach to fully characterize
the dual-primal solutions in such non-commutative setting. The mathematical formalism
is particularly relevant in quantum chemistry: numerical realizations of the many-electron
ground-state energy can be computed via a non-commutative version of Sinkhorn
algorithm. Our approach allows to prove convergence and robustness of this algorithm,
which, to our best knowledge, were unknown even in the two marginal case. Our
methods are based on a priori estimates in the dual problem, which we believe
to be of independent interest. Finally, the above results are extended in 1RDMFT
setting, where bosonic or fermionic symmetry conditions are enforced on the problem.'
acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places
and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature
suggestions in the early state of the project. The authors also thank J. Maas and
R. Seiringer for their feedback and useful comments to a first draft of the article.
Finally, we acknowledge the high quality review done by the anonymous referee of
our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F
acknowledges support by the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 716117 and No
694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council
under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of
his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences
and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges
support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the
Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."
article_number: '109963'
article_processing_charge: No
article_type: original
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.
ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 285(4), 109963.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” Journal of Functional
Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.
short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis
285 (2023).
date_created: 2023-05-07T22:01:02Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '15'
department:
- _id: RoSe
- _id: JaMa
doi: 10.1016/j.jfa.2023.109963
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
isi:
- '000990804300001'
intvolume: ' 285'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9792'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '13177'
abstract:
- lang: eng
text: In this note we study the eigenvalue growth of infinite graphs with discrete
spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type
inequalities and that the total measure is finite. In this sense, the associated
operators on these graphs display similarities to elliptic operators on bounded
domains in the continuum. Specifically, we prove lower bounds on the eigenvalue
growth and show by examples that corresponding upper bounds cannot be established.
acknowledgement: The second author was supported by the priority program SPP2026 of
the German Research Foundation (DFG). The fourth author was supported by the German
Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the
German Research Foundation (DFG) via RTG 1523/2.
article_processing_charge: No
article_type: original
author:
- first_name: Bobo
full_name: Hua, Bobo
last_name: Hua
- first_name: Matthias
full_name: Keller, Matthias
last_name: Keller
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361
apa: Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities
and eigenvalue growth on graphs with finite measure. Proceedings of the American
Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361
chicago: Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type
Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings
of the American Mathematical Society. American Mathematical Society, 2023.
https://doi.org/10.1090/proc/14361.
ieee: B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and
eigenvalue growth on graphs with finite measure,” Proceedings of the American
Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp.
3401–3414, 2023.
ista: Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue
growth on graphs with finite measure. Proceedings of the American Mathematical
Society. 151(8), 3401–3414.
mla: Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs
with Finite Measure.” Proceedings of the American Mathematical Society,
vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.
short: B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical
Society 151 (2023) 3401–3414.
date_created: 2023-07-02T22:00:43Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-11-14T13:07:09Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/proc/14361
external_id:
arxiv:
- '1804.08353'
isi:
- '000988204400001'
intvolume: ' 151'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1804.08353'
month: '08'
oa: 1
oa_version: Preprint
page: 3401-3414
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sobolev-type inequalities and eigenvalue growth on graphs with finite measure
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
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 MH, 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. H., 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 H 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. H. 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 MH, 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.H. 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: 2023-11-20T08:21:07Z
day: '01'
department:
- _id: MoHe
doi: 10.1137/21M1428649
ec_funded: 1
intvolume: ' 52'
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: Wittgenstein Award - Monika Henzinger
- _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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
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
date_created: 2023-11-19T23:00:56Z
date_published: 2023-10-22T00:00:00Z
date_updated: 2023-11-20T08:30:20Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-031-45329-8_17
ec_funded: 1
intvolume: ' 14215'
language:
- iso: eng
month: '10'
oa_version: None
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14215
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.'
date_created: 2023-11-19T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-11-20T08:38:47Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1051/m2an/2023077
ec_funded: 1
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
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: No
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. 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. 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., 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, 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 (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-20T08:51:09Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.14242
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: epub_ahead
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T08:44:17Z
day: '31'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3389/fcell.2023.1287420
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'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14543'
abstract:
- lang: eng
text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed,
plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation
of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function
in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology.
Utilizing exome sequencing and extensive international data sharing efforts, we
identified 45 affected individuals from 28 unrelated families (consanguinity 93%)
with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in
ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9
and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical
proteomics in the model organisms and human cells, with the latter also being
subjected further to ACBD6 peroxisomal localization studies. The affected individuals
(23 males and 22 females), with ages ranging from 1 to 50 years old, typically
present with a complex and progressive disease involving moderate-to-severe global
developmental delay/intellectual disability (100%) with significant expressive
language impairment (98%), movement disorders (97%), facial dysmorphism (95%),
and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia
(76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%),
microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement
disorder was dystonia (94%), frequently leading to early-onset progressive postural
deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor
in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing
with advancing age (32%), and simple motor and vocal tics were among other frequent
movement disorders. Midline brain malformations including corpus callosum abnormalities
(70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and
small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava
(24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus
models effectively recapitulated many clinical phenotypes reported in patients
including movement disorders, progressive neuromotor impairment, seizures, microcephaly,
craniofacial dysmorphism, and midbrain defects accompanied by developmental delay
with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal
localisation and ACBD6-deficiency was not associated with altered peroxisomal
parameters in patient fibroblasts. Significant differences in YnMyr-labelling
were observed for 68 co- and 18 post-translationally N-myristoylated proteins
in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient
zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related
proteins implicated in neurological diseases. The present study provides evidence
that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental
syndrome accompanied by complex and progressive cognitive and movement disorders.
article_number: awad380
article_processing_charge: No
article_type: original
author:
- first_name: Rauan
full_name: Kaiyrzhanov, Rauan
last_name: Kaiyrzhanov
- first_name: Aboulfazl
full_name: Rad, Aboulfazl
last_name: Rad
- first_name: Sheng-Jia
full_name: Lin, Sheng-Jia
last_name: Lin
- first_name: Aida
full_name: Bertoli-Avella, Aida
last_name: Bertoli-Avella
- first_name: Wouter W
full_name: Kallemeijn, Wouter W
last_name: Kallemeijn
- first_name: Annie
full_name: Godwin, Annie
last_name: Godwin
- first_name: Maha S
full_name: Zaki, Maha S
last_name: Zaki
- first_name: Kevin
full_name: Huang, Kevin
id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
last_name: Huang
orcid: 0000-0002-2512-7812
- first_name: Tracy
full_name: Lau, Tracy
last_name: Lau
- first_name: Cassidy
full_name: Petree, Cassidy
last_name: Petree
- first_name: Stephanie
full_name: Efthymiou, Stephanie
last_name: Efthymiou
- first_name: Ehsan
full_name: Ghayoor Karimiani, Ehsan
last_name: Ghayoor Karimiani
- first_name: Maja
full_name: Hempel, Maja
last_name: Hempel
- first_name: Elizabeth A
full_name: Normand, Elizabeth A
last_name: Normand
- first_name: Sabine
full_name: Rudnik-Schöneborn, Sabine
last_name: Rudnik-Schöneborn
- first_name: Ulrich A
full_name: Schatz, Ulrich A
last_name: Schatz
- first_name: Marc P
full_name: Baggelaar, Marc P
last_name: Baggelaar
- first_name: Muhammad
full_name: Ilyas, Muhammad
last_name: Ilyas
- first_name: Tipu
full_name: Sultan, Tipu
last_name: Sultan
- first_name: Javeria Raza
full_name: Alvi, Javeria Raza
last_name: Alvi
- first_name: Manizha
full_name: Ganieva, Manizha
last_name: Ganieva
- first_name: Ben
full_name: Fowler, Ben
last_name: Fowler
- first_name: Ruxandra
full_name: Aanicai, Ruxandra
last_name: Aanicai
- first_name: Gulsen
full_name: Akay Tayfun, Gulsen
last_name: Akay Tayfun
- first_name: Abdulaziz
full_name: Al Saman, Abdulaziz
last_name: Al Saman
- first_name: Abdulrahman
full_name: Alswaid, Abdulrahman
last_name: Alswaid
- first_name: Nafise
full_name: Amiri, Nafise
last_name: Amiri
- first_name: Nilufar
full_name: Asilova, Nilufar
last_name: Asilova
- first_name: Vorasuk
full_name: Shotelersuk, Vorasuk
last_name: Shotelersuk
- first_name: Patra
full_name: Yeetong, Patra
last_name: Yeetong
- first_name: Matloob
full_name: Azam, Matloob
last_name: Azam
- first_name: Meisam
full_name: Babaei, Meisam
last_name: Babaei
- first_name: Gholamreza
full_name: Bahrami Monajemi, Gholamreza
last_name: Bahrami Monajemi
- first_name: Pouria
full_name: Mohammadi, Pouria
last_name: Mohammadi
- first_name: Saeed
full_name: Samie, Saeed
last_name: Samie
- first_name: Selina Husna
full_name: Banu, Selina Husna
last_name: Banu
- first_name: Jorge Pinto
full_name: Basto, Jorge Pinto
last_name: Basto
- first_name: Fanny
full_name: Kortüm, Fanny
last_name: Kortüm
- first_name: Mislen
full_name: Bauer, Mislen
last_name: Bauer
- first_name: Peter
full_name: Bauer, Peter
last_name: Bauer
- first_name: Christian
full_name: Beetz, Christian
last_name: Beetz
- first_name: Masoud
full_name: Garshasbi, Masoud
last_name: Garshasbi
- first_name: Awatif
full_name: Hameed Issa, Awatif
last_name: Hameed Issa
- first_name: Wafaa
full_name: Eyaid, Wafaa
last_name: Eyaid
- first_name: Hind
full_name: Ahmed, Hind
last_name: Ahmed
- first_name: Narges
full_name: Hashemi, Narges
last_name: Hashemi
- first_name: Kazem
full_name: Hassanpour, Kazem
last_name: Hassanpour
- first_name: Isabella
full_name: Herman, Isabella
last_name: Herman
- first_name: Sherozjon
full_name: Ibrohimov, Sherozjon
last_name: Ibrohimov
- first_name: Ban A
full_name: Abdul-Majeed, Ban A
last_name: Abdul-Majeed
- first_name: Maria
full_name: Imdad, Maria
last_name: Imdad
- first_name: Maksudjon
full_name: Isrofilov, Maksudjon
last_name: Isrofilov
- first_name: Qassem
full_name: Kaiyal, Qassem
last_name: Kaiyal
- first_name: Suliman
full_name: Khan, Suliman
last_name: Khan
- first_name: Brian
full_name: Kirmse, Brian
last_name: Kirmse
- first_name: Janet
full_name: Koster, Janet
last_name: Koster
- first_name: Charles Marques
full_name: Lourenço, Charles Marques
last_name: Lourenço
- first_name: Tadahiro
full_name: Mitani, Tadahiro
last_name: Mitani
- first_name: Oana
full_name: Moldovan, Oana
last_name: Moldovan
- first_name: David
full_name: Murphy, David
last_name: Murphy
- first_name: Maryam
full_name: Najafi, Maryam
last_name: Najafi
- first_name: Davut
full_name: Pehlivan, Davut
last_name: Pehlivan
- first_name: Maria Eugenia
full_name: Rocha, Maria Eugenia
last_name: Rocha
- first_name: Vincenzo
full_name: Salpietro, Vincenzo
last_name: Salpietro
- first_name: Miriam
full_name: Schmidts, Miriam
last_name: Schmidts
- first_name: Adel
full_name: Shalata, Adel
last_name: Shalata
- first_name: Mohammad
full_name: Mahroum, Mohammad
last_name: Mahroum
- first_name: Jawabreh Kassem
full_name: Talbeya, Jawabreh Kassem
last_name: Talbeya
- first_name: Robert W
full_name: Taylor, Robert W
last_name: Taylor
- first_name: Dayana
full_name: Vazquez, Dayana
last_name: Vazquez
- first_name: Annalisa
full_name: Vetro, Annalisa
last_name: Vetro
- first_name: Hans R
full_name: Waterham, Hans R
last_name: Waterham
- first_name: Mashaya
full_name: Zaman, Mashaya
last_name: Zaman
- first_name: Tina A
full_name: Schrader, Tina A
last_name: Schrader
- first_name: Wendy K
full_name: Chung, Wendy K
last_name: Chung
- first_name: Renzo
full_name: Guerrini, Renzo
last_name: Guerrini
- first_name: James R
full_name: Lupski, James R
last_name: Lupski
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Mohnish
full_name: Suri, Mohnish
last_name: Suri
- first_name: Yalda
full_name: Jamshidi, Yalda
last_name: Jamshidi
- first_name: Kailash P
full_name: Bhatia, Kailash P
last_name: Bhatia
- first_name: Barbara
full_name: Vona, Barbara
last_name: Vona
- first_name: Michael
full_name: Schrader, Michael
last_name: Schrader
- first_name: Mariasavina
full_name: Severino, Mariasavina
last_name: Severino
- first_name: Matthew
full_name: Guille, Matthew
last_name: Guille
- first_name: Edward W
full_name: Tate, Edward W
last_name: Tate
- first_name: Gaurav K
full_name: Varshney, Gaurav K
last_name: Varshney
- first_name: Henry
full_name: Houlden, Henry
last_name: Houlden
- first_name: Reza
full_name: Maroofian, Reza
last_name: Maroofian
citation:
ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. 2023.
doi:10.1093/brain/awad380
apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W.,
Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders. Brain. Oxford
University Press. https://doi.org/10.1093/brain/awad380
chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella,
Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants
Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.”
Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380.
ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental
syndrome with progressive and complex movement disorders,” Brain. Oxford
University Press, 2023.
ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A,
Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M,
Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi
JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri
N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G,
Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C,
Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman
I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse
B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D,
Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW,
Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski
JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M,
Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6
variants lead to a neurodevelopmental syndrome with progressive and complex movement
disorders. Brain., awad380.
mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental
Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380,
Oxford University Press, 2023, doi:10.1093/brain/awad380.
short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A.
Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani,
M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M.
Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun,
A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M.
Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P.
Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa,
W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed,
M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço,
T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro,
M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A.
Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski,
J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino,
M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).
date_created: 2023-11-16T12:36:51Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-20T10:17:32Z
day: '10'
department:
- _id: GradSch
doi: 10.1093/brain/awad380
extern: '1'
keyword:
- Neurology (clinical)
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/brain/awad380
month: '11'
oa: 1
oa_version: Submitted Version
publication: Brain
publication_identifier:
eissn:
- 1460-2156
issn:
- 0006-8950
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive
and complex movement disorders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14542'
abstract:
- lang: eng
text: "It is a remarkable property of BCS theory that the ratio of the energy gap
at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given
by a universal constant, independent of the microscopic details of the fermionic
interaction. This universality has rigorously been proven quite recently in three
spatial dimensions and three different limiting regimes: weak coupling, low density
and high density. The goal of this short note is to extend the universal behavior
to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."
acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully
acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No.
101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber
I6427.
article_number: '2360005 '
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory.
Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x
apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional
BCS theory. Reviews in Mathematical Physics. World Scientific Publishing.
https://doi.org/10.1142/s0129055x2360005x
chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality
in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World
Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.
ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional
BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing,
2023.
ista: Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS
theory. Reviews in Mathematical Physics., 2360005.
mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.”
Reviews in Mathematical Physics, 2360005, World Scientific Publishing,
2023, doi:10.1142/s0129055x2360005x.
short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).
date_created: 2023-11-15T23:48:14Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-20T10:04:38Z
day: '31'
department:
- _id: GradSch
- _id: LaEr
- _id: RoSe
doi: 10.1142/s0129055x2360005x
ec_funded: 1
external_id:
arxiv:
- '2301.05621'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1142/S0129055X2360005X
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Reviews in Mathematical Physics
publication_identifier:
eissn:
- 1793-6659
issn:
- 0129-055X
publication_status: epub_ahead
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality in low-dimensional BCS theory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '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
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).
date_created: 2023-11-19T23:00:54Z
date_published: 2023-10-30T00:00:00Z
date_updated: 2023-11-20T10:26:51Z
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: '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: 2023-11-20T09:24:48Z
day: '01'
department:
- _id: HeEd
doi: 10.2989/16073606.2023.2247731
intvolume: ' 46'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_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
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full_name: Underwood, N.
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last_name: Barbosa
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full_name: Barrett, S.
last_name: Barrett
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full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
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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: 2023-11-20T11:17:34Z
day: '09'
department:
- _id: NiBa
doi: 10.1126/science.adh8830
external_id:
pmid:
- '37943897'
intvolume: ' 382'
issue: '6671'
language:
- iso: eng
month: '11'
oa_version: None
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 382
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.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-20T11:24:34Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.cels.2023.10.007
ec_funded: 1
external_id:
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14579'
abstract:
- lang: eng
text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain
within-population variability in herbivory\" published in Science.\r\n"
article_processing_charge: No
author:
- first_name: William
full_name: Wetzel, William
last_name: Wetzel
citation:
ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117'
apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo.
https://doi.org/10.5281/ZENODO.8133117'
chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.”
Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.'
ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo,
2023.'
ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo,
10.5281/ZENODO.8133117.'
mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.
Zenodo, 2023, doi:10.5281/ZENODO.8133117.'
short: W. Wetzel, (2023).
date_created: 2023-11-20T11:07:45Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-11-20T11:17:33Z
day: '11'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8133117
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133118
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14552'
relation: used_in_publication
status: public
status: public
title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12334'
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.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _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\nThis 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_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- 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: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- 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: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-11-21T08:05:35Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
file:
- access_level: open_access
checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T07:45:54Z
date_updated: 2023-01-23T07:45:54Z
file_id: '12335'
file_name: 2023_ScienceAdvances_Faessler.pdf
file_size: 1756234
relation: main_file
success: 1
file_date_updated: 2023-01-23T07:45:54Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
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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first_name: Florian
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last_name: Fäßler
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first_name: Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
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first_name: Hermann
last_name: Döring
- contributor_type: researcher
first_name: Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- contributor_type: researcher
first_name: Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- contributor_type: researcher
first_name: Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
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
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:05:34Z
day: '21'
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month: '11'
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oa_version: Published Version
project:
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grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
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relation: used_in_publication
status: public
status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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).
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
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date_updated: 2023-11-08T20:23:07Z
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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: '13342'
abstract:
- lang: eng
text: Motile cells moving in multicellular organisms encounter microenvironments
of locally heterogeneous mechanochemical composition. Individual compositional
parameters like chemotactic signals, adhesiveness, and pore sizes are well known
to be sensed by motile cells, providing individual guidance cues for cellular
pathfinding. However, motile cells encounter diverse mechanochemical signals at
the same time, raising the question of how cells respond to locally diverse and
potentially competing signals on their migration routes. Here, we reveal that
motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for
adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using
mammalian immune cells and the amoebaDictyostelium discoideum,
we discover that frequent, rapid and long-distance nucleokinesis is a basic component
of amoeboid pathfinding, enabling cells to reorientate quickly between locally
competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch
and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the
‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired
nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment.
Our findings establish that nucleokinesis is required for amoeboid cell navigation.
Given that motile single-cell amoebae, many immune cells, and some cancer cells
utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis
underlies cellular navigation during unicellular biology, immunity, and disease.
acknowledgement: We thank Christoph Mayr and Bingzhi Wang for initial experiments
on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow
from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry,
EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte
Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of
the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry,
and the Animal Core Facility of the Biomedical Center (BMC) for excellent support.
This study was supported by the Peter Hans Hofschneider Professorship of the foundation
“Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent
within the framework of the German Excellence Initiative (to JR), and the Deutsche
Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to
JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from
the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled
and organized by Projekt DEAL.
article_number: e114557
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Arthur
full_name: Kuznetcov, Arthur
last_name: Kuznetcov
- first_name: Kasia
full_name: Stefanowski, Kasia
last_name: Stefanowski
- first_name: Monika D.
full_name: Hermann, Monika D.
last_name: Hermann
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Annette
full_name: Müller-Taubenberger, Annette
last_name: Müller-Taubenberger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557
apa: Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin,
J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid
migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557
chicago: Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika
D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg
Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.”
EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.
ieee: J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid
migration,” EMBO Journal. Embo Press, 2023.
ista: Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek
LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal., e114557.
mla: Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid
Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.
short: J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin,
L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).
date_created: 2023-08-01T08:59:06Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-27T08:47:45Z
day: '21'
ddc:
- '570'
department:
- _id: NanoFab
- _id: Bio
doi: 10.15252/embj.2023114557
external_id:
pmid:
- '37987147'
file:
- access_level: open_access
checksum: 6261d0041c7e8d284c39712c40079730
content_type: application/pdf
creator: dernst
date_created: 2023-11-27T08:45:56Z
date_updated: 2023-11-27T08:45:56Z
file_id: '14611'
file_name: 2023_EmboJournal_Kroll.pdf
file_size: 4862497
relation: main_file
success: 1
file_date_updated: 2023-11-27T08:45:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive pathfinding by nucleokinesis during amoeboid migration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14610'
abstract:
- lang: eng
text: AbstractEndomembrane damage represents a
form of stress that is detrimental for eukaryotic cells1,2.
To cope with this threat, cells possess mechanisms that repair the damage and
restore cellular homeostasis3–7. Endomembrane damage also
results in organelle instability and the mechanisms by which cells stabilize damaged
endomembranes to enable membrane repair remains unknown. Here, by combining in
vitro and in cellulo studies with computational modelling we uncover a biological
function for stress granules whereby these biomolecular condensates form rapidly
at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane.
Functionally, we demonstrate that stress granule formation and membrane stabilization
enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal
sorting complex required for transport)-dependent and independent mechanisms.
We also show that blocking stress granule formation in human macrophages creates
a permissive environment for Mycobacterium tuberculosis,
a human pathogen that exploits endomembrane damage to survive within the host.
acknowledgement: "We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy
and High-throughput Screening facilities at the Crick for their support in various
aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO
U2OS cells. The authors thank N. Chen for providing the purified glycinin protein;
Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for
helpful discussions and valuable input regarding analysis methods. This work was
supported by the Francis Crick Institute (to M.G.G.), which receives its core funding
from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and
the Wellcome Trust (FC001092). This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from
the European Respiratory Society and the European Union’s H2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges
support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding
by the Royal Society and the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations
were carried out on the high-performance computing cluster at the Institute of Science
and Technology Austria. For the purpose of Open Access, the author has applied a
CC BY public copyright licence to any Author Accepted Manuscript version arising
from this submission.\r\nOpen Access funding provided by The Francis Crick Institute."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Claudio
full_name: Bussi, Claudio
last_name: Bussi
- first_name: Agustín
full_name: Mangiarotti, Agustín
last_name: Mangiarotti
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Beren
full_name: Aylan, Beren
last_name: Aylan
- first_name: Enrica
full_name: Pellegrino, Enrica
last_name: Pellegrino
- first_name: Natalia
full_name: Athanasiadi, Natalia
last_name: Athanasiadi
- first_name: Antony
full_name: Fearns, Antony
last_name: Fearns
- first_name: Angela
full_name: Rodgers, Angela
last_name: Rodgers
- first_name: Titus M.
full_name: Franzmann, Titus M.
last_name: Franzmann
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Maximiliano G.
full_name: Gutierrez, Maximiliano G.
last_name: Gutierrez
citation:
ama: Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and
stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w
apa: Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino,
E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w
chicago: Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos,
Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress
Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.
ieee: C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal
membranes,” Nature. Springer Nature, 2023.
ista: Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi
N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress
granules plug and stabilize damaged endolysosomal membranes. Nature.
mla: Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal
Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.
short: C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino,
N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G.
Gutierrez, Nature (2023).
date_created: 2023-11-27T07:56:37Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-27T09:05:08Z
day: '15'
department:
- _id: AnSa
doi: 10.1038/s41586-023-06726-w
external_id:
pmid:
- '37968398'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-023-06726-w
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-023-06882-z
record:
- id: '14472'
relation: research_data
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14472'
abstract:
- lang: eng
text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize
damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract:
\r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic
cells. To cope with this threat, cells possess mechanisms that repair the damage
and restore cellular homeostasis. Endomembrane damage also results in organelle
instability and the mechanisms by which cells stabilize damaged endomembranes
to enable membrane repair remains unknown. In this work we use a minimal coarse-grained
molecular dynamics system to explore how lipid vesicles undergoing poration in
a protein-rich medium can be plugged and stabilised by condensate formation. The
solution of proteins in and out of the vesicle is described by beads dispersed
in implicit solvent. The membrane is described as a one-bead-thick fluid elastic
layer of mechanical properties that mimic biological membranes. We tune the interactions
between solution beads in the different compartments to capture the differences
between the cytoplasmic and endosomal protein solutions and explore how the system
responds to different degrees of membrane poration. We find that, in the right
interaction regime, condensates form rapidly at the damage site upon solution
mixing and act as a plug that prevents futher mixing and destabilisation of the
vesicle. Further, when the condensate can interact with the membrane (wetting
interactions) we find that it mediates pore sealing and membrane repair. This
research is part of the work published in \"Stress granules plug and stabilize
damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."
article_processing_charge: No
author:
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal
membranes. 2023. doi:10.15479/AT:ISTA:14472
apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:14472
chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules
Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.
ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged
endolysosomal membranes.” Institute of Science and Technology Austria, 2023.
ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged
endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.
mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug
and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14472.
short: C.E. Vanhille-Campos, A. Šarić, (2023).
date_created: 2023-10-30T16:38:32Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-27T09:05:07Z
day: '31'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.15479/AT:ISTA:14472
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oa: 1
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publisher: Institute of Science and Technology Austria
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relation: used_in_publication
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12747'
abstract:
- lang: eng
text: Muscle degeneration is the most prevalent cause for frailty and dependency
in inherited diseases and ageing. Elucidation of pathophysiological mechanisms,
as well as effective treatments for muscle diseases, represents an important goal
in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine
cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency
in PCYT2 causes a severe disease with failure to thrive and progressive weakness.
pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the
participant phenotypes, with failure to thrive, progressive muscle weakness and
accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular
bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity
declines in ageing muscles of mice and humans, and adeno-associated virus-based
delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice,
offering a therapy for individuals with a rare disease and muscle ageing. Thus,
PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking
PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
acknowledgement: 'The authors thank the participants and their families for participating
in the study. We thank all members of our laboratories for helpful discussions.
We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology
Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative
Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T.
Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A.
Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank
A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg,
Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul
D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector
Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson
(University of Iowa, Carver College of Medicine) for advice on muscle tissue handling.
We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment
of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry
of Education, Science and Research, the Austrian Academy of Sciences, and the City
of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z
271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program
(F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US
National Institutes of Health. C.K. is supported by a grant from the Agence Nationale
de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by
Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by
a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the
laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European
Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative
2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y.
acknowledge the support of the Spastic Paraplegia Foundation.'
article_processing_charge: No
article_type: original
author:
- first_name: Domagoj
full_name: Cikes, Domagoj
last_name: Cikes
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Erdinc
full_name: Sezgin, Erdinc
last_name: Sezgin
- first_name: Erika
full_name: Koitai, Erika
last_name: Koitai
- first_name: Torma
full_name: Ferenc, Torma
last_name: Ferenc
- first_name: Michael
full_name: Orthofer, Michael
last_name: Orthofer
- first_name: Rebecca
full_name: Yarwood, Rebecca
last_name: Yarwood
- first_name: Leonhard X.
full_name: Heinz, Leonhard X.
last_name: Heinz
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: Adrian
full_name: Taylor, Adrian
last_name: Taylor
- first_name: Sophie
full_name: Grapentine, Sophie
last_name: Grapentine
- first_name: Fathiya
full_name: al-Murshedi, Fathiya
last_name: al-Murshedi
- first_name: Anne
full_name: Abot, Anne
last_name: Abot
- first_name: Adelheid
full_name: Weidinger, Adelheid
last_name: Weidinger
- first_name: Candice
full_name: Kutchukian, Candice
last_name: Kutchukian
- first_name: Colline
full_name: Sanchez, Colline
last_name: Sanchez
- first_name: Shane J. F.
full_name: Cronin, Shane J. F.
last_name: Cronin
- first_name: Maria
full_name: Novatchkova, Maria
last_name: Novatchkova
- first_name: Anoop
full_name: Kavirayani, Anoop
last_name: Kavirayani
- first_name: Thomas
full_name: Schuetz, Thomas
last_name: Schuetz
- first_name: Bernhard
full_name: Haubner, Bernhard
last_name: Haubner
- first_name: Lisa
full_name: Haas, Lisa
last_name: Haas
- first_name: Astrid
full_name: Hagelkruys, Astrid
last_name: Hagelkruys
- first_name: Suzanne
full_name: Jackowski, Suzanne
last_name: Jackowski
- first_name: Andrey
full_name: Kozlov, Andrey
last_name: Kozlov
- first_name: Vincent
full_name: Jacquemond, Vincent
last_name: Jacquemond
- first_name: Claude
full_name: Knauf, Claude
last_name: Knauf
- first_name: Giulio
full_name: Superti-Furga, Giulio
last_name: Superti-Furga
- first_name: Eric
full_name: Rullman, Eric
last_name: Rullman
- first_name: Thomas
full_name: Gustafsson, Thomas
last_name: Gustafsson
- first_name: John
full_name: McDermot, John
last_name: McDermot
- first_name: Martin
full_name: Lowe, Martin
last_name: Lowe
- first_name: Zsolt
full_name: Radak, Zsolt
last_name: Radak
- first_name: Jeffrey S.
full_name: Chamberlain, Jeffrey S.
last_name: Chamberlain
- first_name: Marica
full_name: Bakovic, Marica
last_name: Bakovic
- first_name: Siddharth
full_name: Banka, Siddharth
last_name: Banka
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
citation:
ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is
critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515.
doi:10.1038/s42255-023-00766-2
apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., …
Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle
health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2
chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc,
Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis
Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature,
2023. https://doi.org/10.1038/s42255-023-00766-2.
ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to
muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature,
pp. 495–515, 2023.
ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz
LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot
A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani
A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond
V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak
Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid
biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.
mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle
Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp.
495–515, doi:10.1038/s42255-023-00766-2.
short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood,
L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi,
A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova,
A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A.
Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson,
J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger,
Nature Metabolism 5 (2023) 495–515.
date_created: 2023-03-23T12:58:43Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-11-28T07:31:33Z
day: '20'
department:
- _id: Bio
doi: 10.1038/s42255-023-00766-2
external_id:
isi:
- '000992064000002'
pmid:
- '36941451'
intvolume: ' 5'
isi: 1
keyword:
- Cell Biology
- Physiology (medical)
- Endocrinology
- Diabetes and Metabolism
- Internal Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.02.482658
month: '03'
oa: 1
oa_version: Preprint
page: 495-515
pmid: 1
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-023-00791-1
scopus_import: '1'
status: public
title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14605'
abstract:
- lang: eng
text: The phonon transport mechanisms and ultralow lattice thermal conductivities
(κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein,
we study the lattice dynamics and thermal property of AgX under the framework
of perturbation theory and the two-channel Wigner thermal transport model based
on accurate machine learning potentials. We find that an accurate extraction of
the third-order atomic force constants from largely displaced configurations is
significant for the calculation of the κL of AgX, and the coherence thermal transport
is also non-negligible. In AgI, however, the calculated κL still considerably
overestimates the experimental values even including four-phonon scatterings.
Molecular dynamics (MD) simulations using machine learning potential suggest an
important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency
phonon linewidths of AgI at room temperature, which can be related to the simultaneous
restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated
using MD phonon lifetimes including full-order lattice anharmonicity shows a better
agreement with experiments.
acknowledgement: This work is supported by the Research Grants Council of Hong Kong
(Grants No. 17318122 and No. 17306721). The authors are grateful for the research
computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant
Agreement No. 101034413.
article_number: '174302'
article_processing_charge: No
article_type: original
author:
- first_name: Niuchang
full_name: Ouyang, Niuchang
last_name: Ouyang
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
- first_name: Chen
full_name: Wang, Chen
last_name: Wang
- first_name: Qi
full_name: Wang, Qi
last_name: Wang
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
citation:
ama: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity
in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical
Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302
apa: Ouyang, N., Zeng, Z., Wang, C., Wang, Q., & Chen, Y. (2023). Role of high-order
lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br,
I). Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302
chicago: Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of
High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide
AgX (X=Cl,Br, I).” Physical Review B. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevB.108.174302.
ieee: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),”
Physical Review B, vol. 108, no. 17. American Physical Society, 2023.
ista: Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice
anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I).
Physical Review B. 108(17), 174302.
mla: Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon
Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B,
vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.
short: N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2023-11-28T07:48:55Z
day: '01'
department:
- _id: BiCh
doi: 10.1103/PhysRevB.108.174302
ec_funded: 1
intvolume: ' 108'
issue: '17'
language:
- iso: eng
month: '11'
oa_version: None
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of high-order lattice anharmonicity in the phonon thermal transport of
silver halide AgX (X=Cl,Br, I)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '14609'
abstract:
- lang: eng
text: "Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems
without a trusted party. DKG is an essential building block to many decentralized
protocols such as randomness beacons, threshold signatures, Byzantine consensus,
and multiparty computation. While significant progress has been made recently,
existing asynchronous DKG constructions are inefficient when the reconstruction
threshold is larger than one-third of the total nodes. In this paper, we present
a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t
+ 1 nodes that can tolerate up to t malicious nodes and support any reconstruction
threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where
κ is the security parameter, and only assumes the hardness of the Discrete Logarithm.
The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret
share a random polynomial of degree ℓ ≥ t, which has other applications, such
as asynchronous proactive secret sharing and asynchronous multiparty computation.
We implement our high-threshold ADKG protocol and evaluate it using a network
of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold
ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over
the state-of-the-art."
acknowledgement: The authors would like to thank Amit Agarwal, Andrew Miller, and
Tom Yurek for the helpful discussions related to the paper. This work is funded
in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship,
the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.
article_processing_charge: No
author:
- first_name: Sourav
full_name: Das, Sourav
last_name: Das
- first_name: Zhuolun
full_name: Xiang, Zhuolun
last_name: Xiang
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Ling
full_name: Ren, Ling
last_name: Ren
citation:
ama: 'Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. In: 32nd USENIX
Security Symposium. Vol 8. Usenix; 2023:5359-5376.'
apa: 'Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous
high-threshold distributed key generation and distributed polynomial sampling.
In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA,
United States: Usenix.'
chicago: Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical
Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial
Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023.
ieee: S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling,” in 32nd USENIX
Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.
ista: Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold
distributed key generation and distributed polynomial sampling. 32nd USENIX Security
Symposium. USENIX Security Symposium vol. 8, 5359–5376.
mla: Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key
Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium,
vol. 8, Usenix, 2023, pp. 5359–76.
short: S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium,
Usenix, 2023, pp. 5359–5376.
conference:
end_date: 2023-08-11
location: Anaheim, CA, United States
name: USENIX Security Symposium
start_date: 2023-08-09
date_created: 2023-11-26T23:00:55Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-11-28T09:17:38Z
day: '15'
ddc:
- '000'
department:
- _id: ElKo
file:
- access_level: open_access
checksum: 1a730765930138e23c6efd2575872641
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T09:14:34Z
date_updated: 2023-11-28T09:14:34Z
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file_name: 2023_USENIX_Das.pdf
file_size: 704331
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has_accepted_license: '1'
intvolume: ' 8'
language:
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main_file_link:
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url: https://eprint.iacr.org/2022/1389
month: '08'
oa: 1
oa_version: Published Version
page: 5359-5376
project:
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Secure Network and Hardware for Efficient Blockchains
publication: 32nd USENIX Security Symposium
publication_identifier:
isbn:
- '9781713879497'
publication_status: published
publisher: Usenix
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical asynchronous high-threshold distributed key generation and distributed
polynomial sampling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14603'
abstract:
- lang: eng
text: Computing the solubility of crystals in a solvent using atomistic simulations
is notoriously challenging due to the complexities and convergence issues associated
with free-energy methods, as well as the slow equilibration in direct-coexistence
simulations. This paper introduces a molecular-dynamics workflow that simplifies
and robustly computes the solubility of molecular or ionic crystals. This method
is considerably more straightforward than the state-of-the-art, as we have streamlined
and optimised each step of the process. Specifically, we calculate the chemical
potential of the crystal using the gas-phase molecule as a reference state, and
employ the S0 method to determine the concentration dependence of the chemical
potential of the solute. We use this workflow to predict the solubilities of sodium
chloride in water, urea polymorphs in water, and paracetamol polymorphs in both
water and ethanol. Our findings indicate that the predicted solubility is sensitive
to the chosen potential energy surface. Furthermore, we note that the harmonic
approximation often fails for both molecular crystals and gas molecules at or
above room temperature, and that the assumption of an ideal solution becomes less
valid for highly soluble substances.
acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2
system operated by the University of Cambridge Research Computing Service funded
by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from
the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.
article_number: '184110'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Pin Yu
full_name: Chew, Pin Yu
last_name: Chew
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for
computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 2023;159(18). doi:10.1063/5.0173341
apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341
chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics
Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal
of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.
ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals,” Journal
of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.
ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 159(18), 184110.
mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing
Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics,
vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.
short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-14T00:00:00Z
date_updated: 2023-11-28T08:39:23Z
day: '14'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0173341
external_id:
arxiv:
- '2308.10886'
file:
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checksum: f668ee0d07096eef81159d05bc27aabc
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creator: dernst
date_created: 2023-11-28T08:39:06Z
date_updated: 2023-11-28T08:39:06Z
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file_name: 2023_JourChemicalPhysics_Reinhardt.pdf
file_size: 6276059
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file_date_updated: 2023-11-28T08:39:06Z
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month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Chemical Physics
publication_identifier:
eissn:
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issn:
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publisher: AIP Publishing
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title: A streamlined molecular-dynamics workflow for computing solubilities of molecular
and ionic crystals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2023'
...
---
_id: '14604'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years—the oldest known sex chromosome to date. Further, we propose
that the shrinking of gene content the dipteran X chromosome has allowed for a
burst of sex-chromosome turnover that is absent from other speciose insect orders.
acknowledgement: All computational analyses were performed on the server at Institute
of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for
analytical advice, and Tanja Schwander and Vincent Merel for useful discussions.
We also thank Matthew Hahn for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution. Oxford University Press,
2023. https://doi.org/10.1093/evolut/qpad169.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University
Press, pp. 2504–2511, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of class Insecta. Evolution. 77(11), 2504–2511.
mla: Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford
University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.
short: M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '02'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/evolut/qpad169
external_id:
pmid:
- '37738212'
file:
- access_level: open_access
checksum: b66dc10edae92d38918d534e64dda77c
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:12:15Z
date_updated: 2023-11-28T08:12:15Z
file_id: '14618'
file_name: 2023_Evolution_Toups.pdf
file_size: 1399102
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:12:15Z
has_accepted_license: '1'
intvolume: ' 77'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2504-2511
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/bvicoso/veryoldx
record:
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relation: research_data
status: public
- id: '14617'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The X chromosome of insects likely predates the origin of class Insecta
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2023'
...
---
_id: '14616'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Dryad, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:01:53Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:17:31Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5061/DRYAD.HX3FFBGKT
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.hx3ffbgkt
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
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short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14617'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5281/ZENODO.8138705
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Zenodo, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:04:03Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5281/ZENODO.8138705
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8138705
month: '09'
oa: 1
oa_version: Published Version
other_data_license: MIT License
publisher: Zenodo
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14619'
abstract:
- lang: eng
text: Data underlying the publication "A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094'
apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094'
chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.'
ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.'
ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.'
mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.'
short: B. Cheng, (2023).
date_created: 2023-11-28T08:32:18Z
date_published: 2023-10-02T00:00:00Z
date_updated: 2023-11-28T08:39:22Z
day: '02'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.5281/ZENODO.8398094
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8398094
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14603'
relation: used_in_publication
status: public
status: public
title: 'BingqingCheng/solubility: V1.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_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: 2023-11-28T12:04:42Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2022ms003391
file:
- access_level: open_access
checksum: e30329dd985559de0ddc7021ca7382b4
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:29:16Z
date_updated: 2023-11-20T11:29:16Z
file_id: '14582'
file_name: 2023_JAMES_Khoulder.pdf
file_size: 6435697
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:29:16Z
has_accepted_license: '1'
intvolume: ' 15'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '12789'
abstract:
- lang: eng
text: Experiments have shown that charge distributions of granular materials are
non-Gaussian, with broad tails that indicate many particles with high charge.
This observation has consequences for the behavior of granular materials in many
settings, and may bear relevance to the underlying charge transfer mechanism.
However, there is the unaddressed possibility that broad tails arise due to experimental
uncertainties, as determining the shapes of tails is nontrivial. Here we show
that measurement uncertainties can indeed account for most of the tail broadening
previously observed. The clue that reveals this is that distributions are sensitive
to the electric field at which they are measured; ones measured at low (high)
fields have larger (smaller) tails. Accounting for sources of uncertainty, we
reproduce this broadening in silico. Finally, we use our results to back out the
true charge distribution without broadening, which we find is still non-Guassian,
though with substantially different behavior at the tails and indicating significantly
fewer highly charged particles. These results have implications in many natural
settings where electrostatic interactions, especially among highly charged particles,
strongly affect granular behavior.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This research was supported by Grants QUIMAL 160001 and Fondecyt
1221597. This project has received funding from the European Research Council (ERC)
under the European Union's Horizon 2020 research and innovation programme (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of The Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo
Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.
article_number: '034901'
article_processing_charge: No
article_type: original
author:
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901
apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the
shapes of granular charge distributions. Physical Review E. American Physical
Society. https://doi.org/10.1103/PhysRevE.107.034901
chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the
Shapes of Granular Charge Distributions.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901.
ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of
granular charge distributions,” Physical Review E, vol. 107, no. 3. American
Physical Society, 2023.
ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 107(3), 034901.
mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes
of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3,
034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.
short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-11-28T09:22:25Z
day: '01'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevE.107.034901
ec_funded: 1
external_id:
isi:
- '000992142700001'
file:
- access_level: open_access
checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea
content_type: application/pdf
creator: swaituka
date_created: 2023-11-27T09:51:48Z
date_updated: 2023-11-27T09:51:48Z
file_id: '14612'
file_name: PhysRevE.107.034901 (1).pdf
file_size: 1428631
relation: main_file
success: 1
file_date_updated: 2023-11-27T09:51:48Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accurate determination of the shapes of granular charge distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2023'
...
---
_id: '13238'
abstract:
- lang: eng
text: "We consider a natural problem dealing with weighted packet selection across
a rechargeable link, which e.g., finds applications in cryptocurrency networks.
The capacity of a link (u, v) is determined by how much nodes u and v allocate
for this link. Specifically, the input is a finite ordered sequence of packets
that arrive in both directions along a link. Given (u, v) and a packet of weight
x going from u to v, node u can either accept or reject the packet. If u accepts
the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity
on (u, v) increases by x. If a node rejects the packet, this will entail a cost
affinely linear in the weight of the packet. A link is “rechargeable” in the sense
that the total capacity of the link has to remain constant, but the allocation
of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions.
The goal is to minimise the sum of the capacity injected into the link and the
cost of rejecting packets. We show that the problem is NP-hard, but can be approximated
efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."
acknowledgement: We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful
discussions about different variants of the problem. This work is supported by the
European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025,
the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant
470029389 (FlexNets), 2021–2024.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links
in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023:
Structural Information and Communication Complexity . Vol 13892. Springer
Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26'
apa: 'Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection
for rechargeable links in cryptocurrency networks: Complexity and approximation.
In SIROCCO 2023: Structural Information and Communication Complexity (Vol.
13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26'
chicago: 'Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection
for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.”
In SIROCCO 2023: Structural Information and Communication Complexity ,
13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.'
ieee: 'S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation,” in SIROCCO
2023: Structural Information and Communication Complexity , Alcala de Henares,
Spain, 2023, vol. 13892, pp. 576–594.'
ista: 'Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023:
Structural Information and Communication Complexity . SIROCCO: Structural Information
and Communication Complexity, LNCS, vol. 13892, 576–594.'
mla: 'Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency
Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information
and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94,
doi:10.1007/978-3-031-32733-9_26.'
short: 'S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information
and Communication Complexity , Springer Nature, 2023, pp. 576–594.'
conference:
end_date: 2023-06-09
location: Alcala de Henares, Spain
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2023-06-06
date_created: 2023-07-16T22:01:12Z
date_published: 2023-05-25T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '25'
department:
- _id: KrPi
- _id: KrCh
doi: 10.1007/978-3-031-32733-9_26
ec_funded: 1
external_id:
arxiv:
- '2204.13459'
intvolume: ' 13892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.13459
month: '05'
oa: 1
oa_version: Preprint
page: 576-594
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'SIROCCO 2023: Structural Information and Communication Complexity '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031327322'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Weighted packet selection for rechargeable links in cryptocurrency networks:
Complexity and approximation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13892
year: '2023'
...
---
_id: '14506'
abstract:
- lang: eng
text: "Payment channel networks are a promising approach to improve the scalability
bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel
networks are\r\nefficiency and privacy. Payment channel networks improve efficiency
by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes
in the network, avoiding\r\nthe lengthy process of consensus on the blockchain.
Transacting over payment channel\r\nnetworks also improves privacy as these transactions
are not broadcast to the blockchain.\r\nDespite the influx of recent protocols
built on top of payment channel networks and\r\ntheir analysis, a common shortcoming
of many of these protocols is that they typically\r\nfocus only on either improving
efficiency or privacy, but not both. Another limitation\r\non the efficiency front
is that the models used to model actions, costs and utilities of\r\nusers are
limited or come with unrealistic assumptions.\r\nThis thesis aims to address some
of the shortcomings of recent protocols and algorithms\r\non payment channel networks,
particularly in their privacy and efficiency aspects. We\r\nfirst present a payment
route discovery protocol based on hub labelling and private\r\ninformation retrieval
that hides the route query and is also efficient. We then present\r\na rebalancing
protocol that formulates the rebalancing problem as a linear program\r\nand solves
the linear program using multiparty computation so as to hide the channel\r\nbalances.
The rebalancing solution as output by our protocol is also globally optimal.\r\nWe
go on to develop more realistic models of the action space, costs, and utilities
of\r\nboth existing and new users that want to join the network. In each of these
settings,\r\nwe also develop algorithms to optimise the utility of these users
with good guarantees\r\non the approximation and competitive ratios."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis.
2023. doi:10.15479/14506
apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel
network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506
chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel
Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.
ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network
analysis,” Institute of Science and Technology Austria, 2023.
ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network
analysis. Institute of Science and Technology Austria.
mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network
Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.
short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis,
Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T08:10:43Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '10'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/14506
ec_funded: 1
file:
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checksum: 521c72818d720a52b377207b2ee87b6a
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-11-23T10:29:55Z
date_updated: 2023-11-23T10:29:55Z
file_id: '14598'
file_name: thesis_yeo.zip
file_size: 3037720
relation: source_file
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checksum: 0ed5d16899687aecf13d843c9878c9f2
content_type: application/pdf
creator: cchlebak
date_created: 2023-11-23T10:30:08Z
date_updated: 2023-11-23T10:30:08Z
file_id: '14599'
file_name: thesis_yeo.pdf
file_size: 2717256
relation: main_file
success: 1
file_date_updated: 2023-11-23T10:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '162'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9969'
relation: part_of_dissertation
status: public
- id: '13238'
relation: part_of_dissertation
status: public
- id: '14490'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Advances in efficiency and privacy in payment channel network analysis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14490'
abstract:
- lang: eng
text: Payment channel networks (PCNs) are a promising solution to the scalability
problem of cryptocurrencies. Any two users connected by a payment channel in the
network can theoretically send an unbounded number of instant, costless transactions
between them. Users who are not directly connected can also transact with each
other in a multi-hop fashion. In this work, we study the incentive structure behind
the creation of payment channel networks, particularly from the point of view
of a single user that wants to join the network. We define a utility function
for a new user in terms of expected revenue, expected fees, and the cost of creating
channels, and then provide constant factor approximation algorithms that optimise
the utility function given a certain budget. Additionally, we take a step back
from a single user to the whole network and examine the parameter spaces under
which simple graph topologies form a Nash equilibrium.
acknowledgement: The work was partially supported by the Austrian Science Fund (FWF)
through the project CoRaF (grant 2020388). It was also partially supported by NCN
Grant 2019/35/B/ST6/04138 and ERC Grant 885666.
article_processing_charge: No
author:
- first_name: Zeta
full_name: Avarikioti, Zeta
last_name: Avarikioti
- first_name: Tomasz
full_name: Lizurej, Tomasz
last_name: Lizurej
- first_name: Tomasz
full_name: Michalak, Tomasz
last_name: Michalak
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In:
43rd International Conference on Distributed Computing Systems. Vol 2023.
IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037'
apa: 'Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning
creation games. In 43rd International Conference on Distributed Computing Systems
(Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037'
chicago: Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo.
“Lightning Creation Games.” In 43rd International Conference on Distributed
Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.
ieee: Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation
games,” in 43rd International Conference on Distributed Computing Systems,
Hong Kong, China, 2023, vol. 2023, pp. 603–613.
ista: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games.
43rd International Conference on Distributed Computing Systems. ICDCS: International
Conference on Distributed Computing Systems vol. 2023, 603–613.'
mla: Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International
Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13,
doi:10.1109/ICDCS57875.2023.00037.
short: Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International
Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.
conference:
end_date: 2023-07-21
location: Hong Kong, China
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2023-07-18
date_created: 2023-11-05T23:00:54Z
date_published: 2023-10-11T00:00:00Z
date_updated: 2023-11-30T10:54:51Z
day: '11'
department:
- _id: KrPi
doi: 10.1109/ICDCS57875.2023.00037
external_id:
arxiv:
- '2306.16006'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.16006
month: '10'
oa: 1
oa_version: Preprint
page: 603-613
publication: 43rd International Conference on Distributed Computing Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350339864'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Lightning creation games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...