---
_id: '12548'
abstract:
- lang: eng
text: The limited exchange between human communities is a key factor in preventing
the spread of COVID-19. This paper introduces a digital framework that combines
an integration of real mobility data at the country scale with a series of modeling
techniques and visual capabilities that highlight mobility patterns before and
during the pandemic. The findings not only significantly exhibit mobility trends
and different degrees of similarities at regional and local levels but also provide
potential insight into the emergence of a pandemic on human behavior patterns
and their likely socio-economic impacts.
article_number: '00093'
article_processing_charge: No
author:
- first_name: Mohammad
full_name: Forghani, Mohammad
last_name: Forghani
- first_name: Christophe
full_name: Claramunt, Christophe
last_name: Claramunt
- first_name: Farid
full_name: Karimipour, Farid
id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425
last_name: Karimipour
orcid: 0000-0001-6746-4174
- first_name: Georg
full_name: Heiler, Georg
last_name: Heiler
citation:
ama: 'Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility
network changes observed using mobile phone data during COVID-19 pandemic. In:
2022 IEEE International Conference on Data Mining Workshops. Institute
of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093'
apa: 'Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual
analytics of mobility network changes observed using mobile phone data during
COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops.
Orlando, FL, United States: Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/icdmw58026.2022.00093'
chicago: Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler.
“Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data
during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining
Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.
ieee: M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics
of mobility network changes observed using mobile phone data during COVID-19 pandemic,”
in 2022 IEEE International Conference on Data Mining Workshops, Orlando,
FL, United States, 2023.
ista: 'Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of
mobility network changes observed using mobile phone data during COVID-19 pandemic.
2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference
on Data Mining Workshops, 00093.'
mla: Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed
Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International
Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics
Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.
short: M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International
Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers,
2023.
conference:
end_date: 2022-12-01
location: Orlando, FL, United States
name: 'ICDMW: Conference on Data Mining Workshops'
start_date: 2022-11-28
date_created: 2023-02-14T07:56:21Z
date_published: 2023-02-08T00:00:00Z
date_updated: 2023-08-01T13:15:48Z
day: '08'
ddc:
- '600'
department:
- _id: HeEd
doi: 10.1109/icdmw58026.2022.00093
external_id:
isi:
- '000971492200145'
file:
- access_level: open_access
checksum: c253bee25e6dfe484f96662daa119cb6
content_type: application/pdf
creator: fkarimip
date_created: 2023-02-14T07:58:26Z
date_updated: 2023-02-14T07:58:26Z
file_id: '12549'
file_name: Visual Analysis_Mobility_COVID19 - SocDM2022.pdf
file_size: 1183339
relation: main_file
success: 1
file_date_updated: 2023-02-14T07:58:26Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
publication: 2022 IEEE International Conference on Data Mining Workshops
publication_identifier:
eisbn:
- '9798350346091'
eissn:
- 2375-9259
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
status: public
title: Visual analytics of mobility network changes observed using mobile phone data
during COVID-19 pandemic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12563'
abstract:
- lang: eng
text: 'he approximate graph coloring problem, whose complexity is unresolved in
most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable,
where c≥k. This problem naturally generalizes to promise graph homomorphism problems
and further to promise constraint satisfaction problems. The complexity of these
problems has recently been studied through an algebraic approach. In this paper,
we introduce two new techniques to analyze the complexity of promise CSPs: one
is based on topology and the other on adjunction. We apply these techniques, together
with the previously introduced algebraic approach, to obtain new unconditional
NP-hardness results for a significant class of approximate graph coloring and
promise graph homomorphism problems.'
acknowledgement: "Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant
EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No 101034413. Stanislav Živný was supported by a Royal Society University Research
Fellowship. 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 714532). The paper re\x1Eects only the authors’ views and not
the views of the ERC or the European Commission. "
article_processing_charge: No
article_type: original
author:
- first_name: Andrei
full_name: Krokhin, Andrei
last_name: Krokhin
- first_name: Jakub
full_name: Opršal, Jakub
id: ec596741-c539-11ec-b829-c79322a91242
last_name: Opršal
orcid: 0000-0003-1245-3456
- first_name: Marcin
full_name: Wrochna, Marcin
last_name: Wrochna
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise
constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223
apa: Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and
adjunction in promise constraint satisfaction. SIAM Journal on Computing.
Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223
chicago: Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology
and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing.
Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.
ieee: A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction
in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52,
no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.
ista: Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in
promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.
mla: Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.”
SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial &
Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.
short: A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52
(2023) 38–79.
date_created: 2023-02-16T07:03:52Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T13:11:30Z
day: '01'
department:
- _id: UlWa
doi: 10.1137/20m1378223
ec_funded: 1
external_id:
arxiv:
- '2003.11351'
isi:
- '000955000000001'
intvolume: ' 52'
isi: 1
issue: '1'
keyword:
- General Mathematics
- General Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2003.11351
month: '01'
oa: 1
oa_version: Preprint
page: 38-79
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topology and adjunction in promise constraint satisfaction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2023'
...
---
_id: '12545'
abstract:
- lang: eng
text: We study active surface wetting using a minimal model of bacteria that takes
into account the intrinsic motility diversity of living matter. A mixture of “fast”
and “slow” self-propelled Brownian particles is considered in the presence of
a wall. The evolution of the wetting layer thickness shows an overshoot before
stationarity and its composition evolves in two stages, equilibrating after a
slow elimination of excess particles. Nonmonotonic evolutions are shown to arise
from delayed avalanches towards the dilute phase combined with the emergence of
a transient particle front.
acknowledgement: 'MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID
– Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by
grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.'
article_number: '014608'
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. Wetting dynamics by mixtures of fast and
slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608
apa: Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by
mixtures of fast and slow self-propelled particles. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608
chicago: Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting
Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review
E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.
ieee: M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures
of fast and slow self-propelled particles,” Physical Review E, vol. 107,
no. 1. American Physical Society, 2023.
ista: Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of
fast and slow self-propelled particles. Physical Review E. 107(1), 014608.
mla: Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast
and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1,
014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.
short: M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).
date_created: 2023-02-12T23:00:59Z
date_published: 2023-01-24T00:00:00Z
date_updated: 2023-08-01T13:09:45Z
day: '24'
department:
- _id: GradSch
doi: 10.1103/PhysRevE.107.014608
external_id:
arxiv:
- '2301.01856'
isi:
- '000963909800006'
intvolume: ' 107'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.01856
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wetting dynamics by mixtures of fast and slow self-propelled particles
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12427'
abstract:
- lang: eng
text: 'Let k be a number field and X a smooth, geometrically integral quasi-projective
variety over k. For any linear algebraic group G over k and any G-torsor g : Z
→ X, we observe that if the étale-Brauer obstruction is the only one for strong
approximation off a finite set of places S for all twists of Z by elements in
H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation
off a finite set of places S for X. As an application, we show that any homogeneous
space of the form G/H with G a connected linear algebraic group over k satisfies
strong approximation off the infinite places with étale-Brauer obstruction, under
some compactness assumptions when k is totally real. We also prove more refined
strong approximation results for homogeneous spaces of the form G/H with G semisimple
simply connected and H finite, using the theory of torsors and descent.'
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Balestrieri, Francesca
id: 3ACCD756-F248-11E8-B48F-1D18A9856A87
last_name: Balestrieri
citation:
ama: Balestrieri F. Some remarks on strong approximation and applications to homogeneous
spaces of linear algebraic groups. Proceedings of the American Mathematical
Society. 2023;151(3):907-914. doi:10.1090/proc/15239
apa: Balestrieri, F. (2023). Some remarks on strong approximation and applications
to homogeneous spaces of linear algebraic groups. Proceedings of the American
Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239
chicago: Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications
to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American
Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.
ieee: F. Balestrieri, “Some remarks on strong approximation and applications to
homogeneous spaces of linear algebraic groups,” Proceedings of the American
Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp.
907–914, 2023.
ista: Balestrieri F. 2023. Some remarks on strong approximation and applications
to homogeneous spaces of linear algebraic groups. Proceedings of the American
Mathematical Society. 151(3), 907–914.
mla: Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications
to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American
Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023,
pp. 907–14, doi:10.1090/proc/15239.
short: F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023)
907–914.
date_created: 2023-01-29T23:00:58Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T13:03:32Z
day: '01'
department:
- _id: TiBr
doi: 10.1090/proc/15239
external_id:
isi:
- '000898440000001'
intvolume: ' 151'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.science/hal-03013498/
month: '01'
oa: 1
oa_version: Preprint
page: 907-914
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: Some remarks on strong approximation and applications to homogeneous spaces
of linear algebraic groups
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 151
year: '2023'
...
---
_id: '12567'
abstract:
- lang: eng
text: Single-molecule localization microscopy (SMLM) greatly advances structural
studies of diverse biological tissues. For example, presynaptic active zone (AZ)
nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ
proteins usually relies on epitope preservation using aldehyde-based immunocompetent
fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze
substitution (FS), are widely used for ultrastructural studies of presynaptic
architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native
preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures.
Here, we present a protocol combining the advantages of HPF/FS and direct stochastic
optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ
scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila
melanogaster. Using this standardized model, we tested for preservation of Brp
clusters in different FS protocols compared to classical aldehyde fixation. In
HPF/FS samples, presynaptic boutons were structurally well preserved with ~22%
smaller Brp clusters that allowed quantification of subcluster topology. In summary,
we established a standardized near-to-native preparation and immunohistochemistry
protocol for SMLM analyses of AZ protein clusters in a defined model synapse.
Our protocol could be adapted to study protein arrangements at single-molecule
resolution in other intact tissue preparations.
acknowledgement: This work has been supported by funding of the German Research Foundation
(Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S.,
FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center
(IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by
the University of Leipzig Clinician Scientist Program.
article_number: '2128'
article_processing_charge: No
article_type: original
author:
- first_name: Achmed
full_name: Mrestani, Achmed
last_name: Mrestani
- first_name: Katharina
full_name: Lichter, Katharina
id: 39302e62-fcfc-11ec-8196-8b01447dbd3d
last_name: Lichter
- first_name: Anna Leena
full_name: Sirén, Anna Leena
last_name: Sirén
- first_name: Manfred
full_name: Heckmann, Manfred
last_name: Heckmann
- first_name: Mila M.
full_name: Paul, Mila M.
last_name: Paul
- first_name: Martin
full_name: Pauli, Martin
last_name: Pauli
citation:
ama: Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule
localization microscopy of presynaptic active zones in Drosophila melanogaster
after rapid cryofixation. International Journal of Molecular Sciences.
2023;24(3). doi:10.3390/ijms24032128
apa: Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli,
M. (2023). Single-molecule localization microscopy of presynaptic active zones
in Drosophila melanogaster after rapid cryofixation. International Journal
of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128
chicago: Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann,
Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic
Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International
Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.
ieee: A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli,
“Single-molecule localization microscopy of presynaptic active zones in Drosophila
melanogaster after rapid cryofixation,” International Journal of Molecular
Sciences, vol. 24, no. 3. MDPI, 2023.
ista: Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule
localization microscopy of presynaptic active zones in Drosophila melanogaster
after rapid cryofixation. International Journal of Molecular Sciences. 24(3),
2128.
mla: Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic
Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International
Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.
short: A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International
Journal of Molecular Sciences 24 (2023).
date_created: 2023-02-19T23:00:56Z
date_published: 2023-01-21T00:00:00Z
date_updated: 2023-08-01T13:16:36Z
day: '21'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.3390/ijms24032128
external_id:
isi:
- '000930324700001'
file:
- access_level: open_access
checksum: 69a35dcd3e0249f902ab881b06ee2e58
content_type: application/pdf
creator: dernst
date_created: 2023-02-20T07:09:27Z
date_updated: 2023-02-20T07:09:27Z
file_id: '12569'
file_name: 2023_IJMS_Mrestani.pdf
file_size: 2823025
relation: main_file
success: 1
file_date_updated: 2023-02-20T07:09:27Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-molecule localization microscopy of presynaptic active zones in Drosophila
melanogaster after rapid cryofixation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2023'
...
---
_id: '12566'
abstract:
- lang: eng
text: "Approximate agreement is one of the few variants of consensus that can be
solved in a wait-free manner in asynchronous systems where processes communicate
by reading and writing to shared memory. In this work, we consider a natural generalisation
of approximate agreement on arbitrary undirected connected graphs. Each process
is given a node of the graph as input and, if non-faulty, must output a node such
that\r\n– all the outputs are within distance 1 of one another, and\r\n– each
output value lies on a shortest path between two input values.\r\nFrom prior work,
it is known that there is no wait-free algorithm among processes for this problem
on any cycle of length , by reduction from 2-set agreement (Castañeda et al.,
2018).\r\n\r\nIn this work, we investigate the solvability of this task on general
graphs. We give a new, direct proof of the impossibility of approximate agreement
on cycles of length , via a generalisation of Sperner's Lemma to convex polygons.
We also extend the reduction from 2-set agreement to a larger class of graphs,
showing that approximate agreement on these graphs is unsolvable. On the positive
side, we present a wait-free algorithm for a different class of graphs, which
properly contains the class of chordal graphs."
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. 805223 ScaleML) and under the Marie Skłodowska-Curie grant
agreement No. 840605 and from the Natural Sciences and Engineering Research Council
of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was
visiting IST Austria.
article_number: '113733'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs.
Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733
apa: Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate
agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733
chicago: Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate
Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.
ieee: D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement
on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.
ista: Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on
graphs. Theoretical Computer Science. 948(2), 113733.
mla: Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical
Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.
short: D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).
date_created: 2023-02-19T23:00:55Z
date_published: 2023-02-28T00:00:00Z
date_updated: 2023-08-01T13:17:20Z
day: '28'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2023.113733
ec_funded: 1
external_id:
isi:
- '000934262700001'
file:
- access_level: open_access
checksum: b27c5290f2f1500c403494364ee39c9f
content_type: application/pdf
creator: dernst
date_created: 2023-02-20T07:30:20Z
date_updated: 2023-02-20T07:30:20Z
file_id: '12570'
file_name: 2023_TheoreticalCompScience_Alistarh.pdf
file_size: 602333
relation: main_file
success: 1
file_date_updated: 2023-02-20T07:30:20Z
has_accepted_license: '1'
intvolume: ' 948'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wait-free approximate agreement on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 948
year: '2023'
...
---
_id: '12681'
abstract:
- lang: eng
text: The dissolution of minute concentration of polymers in wall-bounded flows
is well-known for its unparalleled ability to reduce turbulent friction drag.
Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied
even though elastic instabilities have already been observed in dilute polymer
solutions before the discovery of polymer drag reduction. EIT is a chaotic state
driven by polymer dynamics that is observed across many orders of magnitude in
Reynolds number. It involves energy transfer from small elastic scales to large
flow scales. The investigation of the mechanisms of EIT offers the possibility
to better understand other complex phenomena such as elastic turbulence and maximum
drag reduction. In this review, we survey recent research efforts that are advancing
the understanding of the dynamics of EIT. We highlight the fundamental differences
between EIT and Newtonian/inertial turbulence from the perspective of experiments,
numerical simulations, instabilities, and coherent structures. Finally, we discuss
the possible links between EIT and elastic turbulence and polymer drag reduction,
as well as the remaining challenges in unraveling the self-sustaining mechanism
of EIT.
acknowledgement: Part of the material presented here is based upon work supported
by the National Science Foundation CBET (Chemical, Bioengineering, Environmental
and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation
award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training
in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for
Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073
(to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University
of Liege (to V.E.T.). Computational resources have been provided by the Consortium
des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the
Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing
in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles
funded by the Walloon Region (grant agreement 117545).
article_processing_charge: No
article_type: original
author:
- first_name: Yves
full_name: Dubief, Yves
last_name: Dubief
- first_name: Vincent E.
full_name: Terrapon, Vincent E.
last_name: Terrapon
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review
of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933
apa: Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence.
Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933
chicago: Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.”
Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.
ieee: Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual
Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.
ista: Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review
of Fluid Mechanics. 55(1), 675–705.
mla: Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid
Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.
short: Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023)
675–705.
date_created: 2023-02-26T23:01:01Z
date_published: 2023-01-19T00:00:00Z
date_updated: 2023-08-01T13:19:47Z
day: '19'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1146/annurev-fluid-032822-025933
external_id:
isi:
- '000915418100026'
file:
- access_level: open_access
checksum: 2666aa3af2a25252d35eb8681d3edff7
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T09:23:02Z
date_updated: 2023-02-27T09:23:02Z
file_id: '12690'
file_name: 2023_AnnReviewFluidMech_Dubief.pdf
file_size: 4036706
relation: main_file
success: 1
file_date_updated: 2023-02-27T09:23:02Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 675-705
publication: Annual Review of Fluid Mechanics
publication_identifier:
eissn:
- 1545-4479
issn:
- 0066-4189
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Elasto-inertial turbulence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 55
year: '2023'
...
---
_id: '12682'
abstract:
- lang: eng
text: 'Since the seminal studies by Osborne Reynolds in the nineteenth century,
pipe flow has served as a primary prototype for investigating the transition to
turbulence in wall-bounded flows. Despite the apparent simplicity of this flow,
various facets of this problem have occupied researchers for more than a century.
Here we review insights from three distinct perspectives: (a) stability and susceptibility
of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical
systems analysis of the Navier—Stokes equations. We show how these perspectives
have led to a profound understanding of the onset of turbulence in pipe flow.
Outstanding open points, applications to flows of complex fluids, and similarities
with other wall-bounded flows are discussed.'
acknowledgement: 'The authors are very grateful to Laurette Tuckerman for her helpful
comments. This work was supported by grants from the Simons Foundation (grant numbers
662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent
Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2
to M.A.).'
article_processing_charge: No
article_type: original
author:
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual
Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957
apa: Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe
flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957
chicago: Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in
Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957.
ieee: M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,”
Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602,
2023.
ista: Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual
Review of Fluid Mechanics. 55, 575–602.
mla: Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review
of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.
short: M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023)
575–602.
date_created: 2023-02-26T23:01:01Z
date_published: 2023-01-19T00:00:00Z
date_updated: 2023-08-01T13:20:30Z
day: '19'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1146/annurev-fluid-120720-025957
external_id:
isi:
- '000915418100023'
file:
- access_level: open_access
checksum: f99ef30f76cabc9e5e1946b380c16db4
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T09:35:52Z
date_updated: 2023-02-27T09:35:52Z
file_id: '12691'
file_name: 2023_AnnReviewFluidMech_Avila.pdf
file_size: 4769537
relation: main_file
success: 1
file_date_updated: 2023-02-27T09:35:52Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 575-602
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Annual Review of Fluid Mechanics
publication_identifier:
issn:
- 0066-4189
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to turbulence in pipe flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 55
year: '2023'
...
---
_id: '12708'
abstract:
- lang: eng
text: Self-organisation is the spontaneous emergence of spatio-temporal structures
and patterns from the interaction of smaller individual units. Examples are found
across many scales in very different systems and scientific disciplines, from
physics, materials science and robotics to biology, geophysics and astronomy.
Recent research has highlighted how self-organisation can be both mediated and
controlled by confinement. Confinement is an action over a system that limits
its units’ translational and rotational degrees of freedom, thus also influencing
the system's phase space probability density; it can function as either a catalyst
or inhibitor of self-organisation. Confinement can then become a means to actively
steer the emergence or suppression of collective phenomena in space and time.
Here, to provide a common framework and perspective for future research, we examine
the role of confinement in the self-organisation of soft-matter systems and identify
overarching scientific challenges that need to be addressed to harness its full
scientific and technological potential in soft matter and related fields. By drawing
analogies with other disciplines, this framework will accelerate a common deeper
understanding of self-organisation and trigger the development of innovative strategies
to steer it using confinement, with impact on, e.g., the design of smarter materials,
tissue engineering for biomedicine and in guiding active matter.
acknowledgement: 'All authors are grateful to the Lorentz Center for providing a venue
for stimulating scientific discussions and to sponsor a workshop on the topic of
“Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers
Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University
of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan
Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial
support from the Portuguese Foundation for Science and Technology (FCT) under Contracts
no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and
UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands
Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte,
and Vidi grant. I. C. was supported in part by a grant from by the Army Research
Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875).
O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant
No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European
Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges
funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported
by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges
financial support from the Netherlands Organisation for Scientific Research (NWO)
through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck
School Matter to Life and the MaxSynBio Consortium, which are jointly funded by
the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck
Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant
ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO
Talent Programme which is financed by the Dutch Research Council (project number
VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft
(DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding
from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and
ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no.
RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges
financial support from the European Research Council (Grant No. ERC-2018-STG-H2020
802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No.
A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges
funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006
and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant
DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges
funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also
acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and
from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding
from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding
from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges
sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).'
article_processing_charge: No
article_type: original
author:
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Liesbeth M.C.
full_name: Janssen, Liesbeth M.C.
last_name: Janssen
- first_name: Thomas
full_name: Barois, Thomas
last_name: Barois
- first_name: Guido
full_name: Boffetta, Guido
last_name: Boffetta
- first_name: Itai
full_name: Cohen, Itai
last_name: Cohen
- first_name: Alessandro
full_name: Corbetta, Alessandro
last_name: Corbetta
- first_name: Olivier
full_name: Dauchot, Olivier
last_name: Dauchot
- first_name: Marjolein
full_name: Dijkstra, Marjolein
last_name: Dijkstra
- first_name: William M.
full_name: Durham, William M.
last_name: Durham
- first_name: Audrey
full_name: Dussutour, Audrey
last_name: Dussutour
- first_name: Simon
full_name: Garnier, Simon
last_name: Garnier
- first_name: Hanneke
full_name: Gelderblom, Hanneke
last_name: Gelderblom
- first_name: Ramin
full_name: Golestanian, Ramin
last_name: Golestanian
- first_name: Lucio
full_name: Isa, Lucio
last_name: Isa
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Hartmut
full_name: Löwen, Hartmut
last_name: Löwen
- first_name: Ralf
full_name: Metzler, Ralf
last_name: Metzler
- first_name: Marco
full_name: Polin, Marco
last_name: Polin
- first_name: C. Patrick
full_name: Royall, C. Patrick
last_name: Royall
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Anupam
full_name: Sengupta, Anupam
last_name: Sengupta
- first_name: Cécile
full_name: Sykes, Cécile
last_name: Sykes
- first_name: Vito
full_name: Trianni, Vito
last_name: Trianni
- first_name: Idan
full_name: Tuval, Idan
last_name: Tuval
- first_name: Nicolas
full_name: Vogel, Nicolas
last_name: Vogel
- first_name: Julia M.
full_name: Yeomans, Julia M.
last_name: Yeomans
- first_name: Iker
full_name: Zuriguel, Iker
last_name: Zuriguel
- first_name: Alvaro
full_name: Marin, Alvaro
last_name: Marin
- first_name: Giorgio
full_name: Volpe, Giorgio
last_name: Volpe
citation:
ama: Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through
confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e
apa: Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta,
A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e
chicago: Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta,
Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation
through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.
ieee: N. A. M. Araújo et al., “Steering self-organisation through confinement,”
Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.
ista: Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot
O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R,
Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta
A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe
G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.
mla: Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.”
Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.
short: N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta,
O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom,
R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P.
Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M.
Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.
date_created: 2023-03-05T23:01:06Z
date_published: 2023-02-06T00:00:00Z
date_updated: 2023-08-01T13:28:39Z
day: '06'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1039/d2sm01562e
ec_funded: 1
external_id:
arxiv:
- '2204.10059'
isi:
- '000940388100001'
file:
- access_level: open_access
checksum: af95aa18b9b01e32fb8f13477c0e2687
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T09:19:41Z
date_updated: 2023-03-07T09:19:41Z
file_id: '12711'
file_name: 2023_SoftMatter_Araujo.pdf
file_size: 3581939
relation: main_file
success: 1
file_date_updated: 2023-03-07T09:19:41Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1695-1704
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Steering self-organisation through confinement
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '12702'
abstract:
- lang: eng
text: Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation
from them can play a crucial role in shaping the interior structure and evolution
of planets. With first-principles accuracy, we first estimate the melting line
of diamond, and then reveal the nature of chemical bonding in hydrocarbons at
extreme conditions. We finally establish the pressure-temperature phase boundary
where it is thermodynamically possible for diamond to form from hydrocarbon mixtures
with different atomic fractions of carbon. Notably, here we show a depletion zone
at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond
formation is thermodynamically favorable regardless of the carbon atomic fraction,
due to a phase separation mechanism. The cooler condition of the interior of Neptune
compared to Uranus means that the former is much more likely to contain the depletion
zone. Our findings can help explain the dichotomy of the two ice giants manifested
by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary
formation and evolution.
acknowledgement: BC thanks Daan Frenkel for stimulating discussions. We thank Aleks
Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris
J. Pickard for critically reading the manuscript and providing useful suggestions.
BC acknowledges resources provided by the Cambridge Tier-2 system operated by the
University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital
grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support
from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand
Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence
Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear
Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support
by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE
grant number 894725), funding from the NOMIS foundation and computational resources
at the North-German Supercomputing Alliance (HLRN) facilities.
article_number: '1104'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Sebastien
full_name: Hamel, Sebastien
last_name: Hamel
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
citation:
ama: Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from
hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1
apa: Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond
formation from hydrocarbon mixtures in planets. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-36841-1
chicago: Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics
of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.
ieee: B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation
from hydrocarbon mixtures in planets,” Nature Communications, vol. 14.
Springer Nature, 2023.
ista: Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation
from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.
mla: Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon
Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature,
2023, doi:10.1038/s41467-023-36841-1.
short: B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).
date_created: 2023-03-05T23:01:04Z
date_published: 2023-02-27T00:00:00Z
date_updated: 2023-08-01T13:36:11Z
day: '27'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1038/s41467-023-36841-1
external_id:
isi:
- '000939678300002'
pmid:
- '36843123'
file:
- access_level: open_access
checksum: 5ff61ad21511950c15abb73b18613883
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T10:58:00Z
date_updated: 2023-03-07T10:58:00Z
file_id: '12713'
file_name: 2023_NatComm_Cheng.pdf
file_size: 1946443
relation: main_file
success: 1
file_date_updated: 2023-03-07T10:58:00Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermodynamics of diamond formation from hydrocarbon mixtures in planets
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12719'
abstract:
- lang: eng
text: "Background\r\nEpigenetic clocks can track both chronological age (cAge) and
biological age (bAge). The latter is typically defined by physiological biomarkers
and risk of adverse health outcomes, including all-cause mortality. As cohort
sample sizes increase, estimates of cAge and bAge become more precise. Here, we
aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving
our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we
perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of
chronological age and all-cause mortality. Next, to create a cAge predictor, we
use methylation data from 24,674 participants from the Generation Scotland study,
the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly
available data. In addition, we train a predictor of time to all-cause mortality
as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths).
For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins
and the 8 component parts of GrimAge, one of the current best epigenetic predictors
of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936,
the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough
the inclusion of linear and non-linear age-CpG associations from the EWAS, feature
pre-selection in advance of elastic net regression, and a leave-one-cohort-out
(LOCO) cross-validation framework, we obtain cAge prediction with a median absolute
error equal to 2.3 years. Our bAge predictor was found to slightly outperform
GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47
[1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60).
Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide
CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large
datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection
has facilitated improvements to the blood-based epigenetic prediction of biological
and chronological age."
acknowledgement: We are grateful to all the families who took part, the general practitioners,
and the Scottish School of Primary Care for their help in recruiting them and the
whole GS team that includes interviewers, computer and laboratory technicians, clerical
workers, research scientists, volunteers, managers, receptionists, healthcare assistants,
and nurses.
article_number: '12'
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Bernabeu, Elena
last_name: Bernabeu
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Danni A.
full_name: Gadd, Danni A.
last_name: Gadd
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Ake T.
full_name: Lu, Ake T.
last_name: Lu
- first_name: Lee
full_name: Murphy, Lee
last_name: Murphy
- first_name: Nicola
full_name: Wrobel, Nicola
last_name: Wrobel
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: David
full_name: Liewald, David
last_name: Liewald
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Cathie
full_name: Sudlow, Cathie
last_name: Sudlow
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Steve
full_name: Horvath, Steve
last_name: Horvath
- first_name: Andrew M.
full_name: Mcintosh, Andrew M.
last_name: Mcintosh
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Catalina A.
full_name: Vallejos, Catalina A.
last_name: Vallejos
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of
chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y
apa: Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy,
L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and
biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y
chicago: Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary,
Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of
Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023.
https://doi.org/10.1186/s13073-023-01161-y.
ieee: E. Bernabeu et al., “Refining epigenetic prediction of chronological
and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.
ista: Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N,
Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath
S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic
prediction of chronological and biological age. Genome Medicine. 15, 12.
mla: Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and
Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.
short: E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy,
N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox,
K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni,
Genome Medicine 15 (2023).
date_created: 2023-03-12T23:01:02Z
date_published: 2023-02-28T00:00:00Z
date_updated: 2023-08-01T13:38:12Z
day: '28'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-023-01161-y
external_id:
isi:
- '000940286600001'
file:
- access_level: open_access
checksum: 833b837910c4db42fb5f0f34125f77a7
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-14T10:29:47Z
date_updated: 2023-03-14T10:29:47Z
file_id: '12722'
file_name: 2023_GenomeMed_Bernabeu.pdf
file_size: 4275987
relation: main_file
success: 1
file_date_updated: 2023-03-14T10:29:47Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Genome Medicine
publication_identifier:
eissn:
- 1756-994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Refining epigenetic prediction of chronological and biological age
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2023'
...
---
_id: '12704'
abstract:
- lang: eng
text: Adversarial training (i.e., training on adversarially perturbed input data)
is a well-studied method for making neural networks robust to potential adversarial
attacks during inference. However, the improved robustness does not come for free
but rather is accompanied by a decrease in overall model accuracy and performance.
Recent work has shown that, in practical robot learning applications, the effects
of adversarial training do not pose a fair trade-off but inflict a net loss when
measured in holistic robot performance. This work revisits the robustness-accuracy
trade-off in robot learning by systematically analyzing if recent advances in
robust training methods and theory in conjunction with adversarial robot learning,
are capable of making adversarial training suitable for real-world robot applications.
We evaluate three different robot learning tasks ranging from autonomous driving
in a high-fidelity environment amenable to sim-to-real deployment to mobile robot
navigation and gesture recognition. Our results demonstrate that, while these
techniques make incremental improvements on the trade-off on a relative scale,
the negative impact on the nominal accuracy caused by adversarial training still
outweighs the improved robustness by an order of magnitude. We conclude that although
progress is happening, further advances in robust learning methods are necessary
before they can benefit robot learning tasks in practice.
acknowledgement: "We thank Christoph Lampert for inspiring this work. The\r\nviews
and conclusions contained in this document are those of\r\nthe authors and should
not be interpreted as representing the\r\nofficial policies, either expressed or
implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government
is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes
notwithstanding any copyright notation herein."
article_processing_charge: No
article_type: original
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602.
doi:10.1109/LRA.2023.3240930
apa: Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting
the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics
and Automation Letters. Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/LRA.2023.3240930
chicago: Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger.
“Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE
Robotics and Automation Letters. Institute of Electrical and Electronics Engineers,
2023. https://doi.org/10.1109/LRA.2023.3240930.
ieee: M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial
robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation
Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers,
pp. 1595–1602, 2023.
ista: Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial
robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters.
8(3), 1595–1602.
mla: Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff
in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3,
Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.
short: M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation
Letters 8 (2023) 1595–1602.
date_created: 2023-03-05T23:01:04Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:36:50Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/LRA.2023.3240930
external_id:
arxiv:
- '2204.07373'
isi:
- '000936534100012'
file:
- access_level: open_access
checksum: 5a75dcd326ea66685de2b1aaec259e85
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T12:22:23Z
date_updated: 2023-03-07T12:22:23Z
file_id: '12714'
file_name: 2023_IEEERobAutLetters_Lechner.pdf
file_size: 944052
relation: main_file
success: 1
file_date_updated: 2023-03-07T12:22:23Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1595-1602
publication: IEEE Robotics and Automation Letters
publication_identifier:
eissn:
- 2377-3766
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '11366'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Revisiting the adversarial robustness-accuracy tradeoff in robot learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2023'
...
---
_id: '12723'
abstract:
- lang: eng
text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties.
To explain their origin, it is necessary to study how electromagnetic fields interact
with these systems. We address this problem here by studying two classical quantities:
Faraday rotation and the complex refractive index in a paradigmatic perovskite
CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of
electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the
observed data even on the qualitative level. To amend this, we demonstrate that
there exists a relevant atomic-level coupling between electromagnetic fields and
the spin degree of freedom. This spin-electric coupling allows for quantitative
description of a number of previous as well as present experimental data. In particular,
we use it here to show that the Faraday effect in lead halide perovskites is dominated
by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel
contribution. Finally, we present general symmetry-based phenomenological arguments
that in the low-energy limit our effective model includes all basis coupling terms
to the electromagnetic field in the linear order.'
article_number: '106901'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan A.
full_name: Zhumekenov, Ayan A.
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead
halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide
perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev.
“Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.
ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,”
Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites.
Physical Review Letters. 130(10), 106901.
mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.”
Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society,
2023, doi:10.1103/physrevlett.130.106901.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).
date_created: 2023-03-14T13:11:59Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T13:39:04Z
day: '10'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevlett.130.106901
external_id:
arxiv:
- '2203.09443'
isi:
- '000982435900002'
intvolume: ' 130'
isi: 1
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.09443
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-electric coupling in lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12724'
abstract:
- lang: eng
text: 'We use general symmetry-based arguments to construct an effective model suitable
for studying optical properties of lead halide perovskites. To build the model,
we identify an atomic-level interaction between electromagnetic fields and the
spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian.
As a first application, we study two basic optical characteristics of the material:
the Verdet constant and the refractive index. Beyond these linear characteristics
of the material, the model is suitable for calculating nonlinear effects such
as the third-order optical susceptibility. Analysis of this quantity shows that
the geometrical properties of the spin-electric term imply isotropic optical response
of the system, and that optical anisotropy of lead halide perovskites is a manifestation
of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.'
article_number: '125201'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan
full_name: Zhumekenov, Ayan
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical
properties of lead halide perovskites. Physical Review B. 2023;107(12).
doi:10.1103/physrevb.107.125201
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical
properties of lead halide perovskites. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.107.125201
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective
Model for Studying Optical Properties of Lead Halide Perovskites.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.
ieee: A. Volosniev et al., “Effective model for studying optical properties
of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American
Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties
of lead halide perovskites. Physical Review B. 107(12), 125201.
mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of
Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201,
American Physical Society, 2023, doi:10.1103/physrevb.107.125201.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).
date_created: 2023-03-14T13:13:05Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:39:47Z
day: '15'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevb.107.125201
external_id:
arxiv:
- '2204.04022'
isi:
- '000972602200006'
intvolume: ' 107'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.04022
month: '03'
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: Effective model for studying optical properties of lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12759'
abstract:
- lang: eng
text: Stereological methods for estimating the 3D particle size and density from
2D projections are essential to many research fields. These methods are, however,
prone to errors arising from undetected particle profiles due to sectioning and
limited resolution, known as ‘lost caps’. A potential solution developed by Keiding,
Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for
lost caps by quantifying the smallest detectable profile in terms of its limiting
‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the
section surface. However, this simple solution has not been widely adopted nor
tested. Rather, model-independent design-based stereological methods, which do
not explicitly account for lost caps, have come to the fore. Here, we provide
the first experimental validation of the Keiding model by comparing the size and
density of particles estimated from 2D projections with direct measurement from
3D EM reconstructions of the same tissue. We applied the Keiding model to estimate
the size and density of somata, nuclei and vesicles in the cerebellum of mice
and rats, where high packing density can be problematic for design-based methods.
Our analysis reveals a Gaussian distribution for ϕ rather than a single value.
Nevertheless, curve fits of the Keiding model to the 2D diameter distribution
accurately estimate the mean ϕ and 3D diameter distribution. While systematic
testing using simulations revealed an upper limit to determining ϕ, our analysis
shows that estimated ϕ can be used to determine the 3D particle density from the
2D density under a wide range of conditions, and this method is potentially more
accurate than minimum-size-based lost-cap corrections and disector methods. Our
results show the Keiding model provides an efficient means of accurately estimating
the size and density of particles from 2D projections even under conditions of
a high density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical
support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments
and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048;
224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal
Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung
der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z
312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding
from the European Research Council (ERC; https://erc.europa.eu) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692).
NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
full_name: Rothman, Jason Seth
last_name: Rothman
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Noemi
full_name: Holderith, Noemi
last_name: Holderith
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: R.
full_name: Angus Silver, R.
last_name: Angus Silver
citation:
ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation
of a stereological method for estimating particle size and density from 2D projections
with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148
apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus
Silver, R. (2023). Validation of a stereological method for estimating particle
size and density from 2D projections with high accuracy. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0277148
chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M
Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.
ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus
Silver, “Validation of a stereological method for estimating particle size and
density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no.
3 March. Public Library of Science, 2023.
ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023.
Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.
mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE,
vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.
short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:46:39Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
isi:
- '001024737400001'
file:
- access_level: open_access
checksum: 2380331ec27cc87808826fc64419ac1c
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:51:09Z
date_updated: 2023-03-27T06:51:09Z
file_id: '12770'
file_name: 2023_PLoSOne_Rothman.pdf
file_size: 7290413
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
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: Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:45:54Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2023'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
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: Using AlphaFold to predict the impact of single mutations on protein stability
and function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:45:12Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...
---
_id: '12787'
abstract:
- lang: eng
text: "Populations evolve in spatially heterogeneous environments. While a certain
trait might bring a fitness advantage in some patch of the environment, a different
trait might be advantageous in another patch. Here, we study the Moran birth–death
process with two types of individuals in a population stretched across two patches
of size N, each patch favouring one of the two types. We show that the long-term
fate of such populations crucially depends on the migration rate μ\r\n between
the patches. To classify the possible fates, we use the distinction between polynomial
(short) and exponential (long) timescales. We show that when μ is high then one
of the two types fixates on the whole population after a number of steps that
is only polynomial in N. By contrast, when μ is low then each type holds majority
in the patch where it is favoured for a number of steps that is at least exponential
in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates
those two scenarios, thereby exactly delineating the situations that support long-term
coexistence of the two types. We also discuss the case of various cycle graphs
and we present computer simulations that perfectly match our analytical results."
acknowledgement: J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)
article_number: '20220685'
article_processing_charge: No
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran
process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685'
apa: 'Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence
times in the Moran process with environmental heterogeneity. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rspa.2022.0685'
chicago: 'Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee.
“Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.'
ieee: 'J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in
the Moran process with environmental heterogeneity,” Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no.
2271. The Royal Society, 2023.'
ista: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the
Moran process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.'
mla: 'Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental
Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society,
2023, doi:10.1098/rspa.2022.0685.'
short: 'J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences 479 (2023).'
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2023-08-01T13:58:34Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rspa.2022.0685
ec_funded: 1
external_id:
isi:
- '000957125500002'
file:
- access_level: open_access
checksum: 13953d349fbefcb5d21ccc6b303297eb
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:25:29Z
date_updated: 2023-04-03T06:25:29Z
file_id: '12796'
file_name: 2023_ProceedingsRoyalSocietyA_Svoboda.pdf
file_size: 827784
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:25:29Z
has_accepted_license: '1'
intvolume: ' 479'
isi: 1
issue: '2271'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
eissn:
- 1471-2946
issn:
- 1364-5021
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: research_data
url: https://doi.org/10.6084/m9.figshare.21261771.v1
scopus_import: '1'
status: public
title: Coexistence times in the Moran process with environmental heterogeneity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 479
year: '2023'
...
---
_id: '12788'
abstract:
- lang: eng
text: We show that the simplest of existing molecules—closed-shell diatomics not
interacting with one another—host topological charges when driven by periodic
far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped
onto a “crystalline” lattice in angular momentum space. This allows us to define
quasimomenta and the band structure in the Floquet representation, by analogy
with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3
of the molecular rotational period creates a lattice with three atoms per unit
cell with staggered hopping. Within the synthetic dimension of the laser strength,
we discover Dirac cones with topological charges. These Dirac cones, topologically
protected by reflection and time-reversal symmetry, are reminiscent of (although
not equivalent to) that seen in graphene. They—and the corresponding edge states—are
broadly tunable by adjusting the laser strength and can be observed in present-day
experiments by measuring molecular alignment and populations of rotational levels.
This paves the way to study controllable topological physics in gas-phase experiments
with small molecules as well as to classify dynamical molecular states by their
topological invariants.
acknowledgement: M. L. acknowledges support by the European Research Council (ERC)
Starting Grant No. 801770 (ANGULON).
article_number: '103202'
article_processing_charge: No
article_type: original
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
- 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: Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked
molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202
apa: Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of
periodically kicked molecules. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.130.103202
chicago: Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges
of Periodically Kicked Molecules.” Physical Review Letters. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.
ieee: V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically
kicked molecules,” Physical Review Letters, vol. 130, no. 10. American
Physical Society, 2023.
ista: Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically
kicked molecules. Physical Review Letters. 130(10), 103202.
mla: Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.”
Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society,
2023, doi:10.1103/PhysRevLett.130.103202.
short: V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T14:02:06Z
day: '10'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.130.103202
ec_funded: 1
external_id:
arxiv:
- '2206.07067'
isi:
- '000957635500003'
intvolume: ' 130'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2206.07067
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/topology-of-rotating-molecules/
scopus_import: '1'
status: public
title: Topological charges of periodically kicked molecules
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12790'
abstract:
- lang: eng
text: Motivated by the recent discoveries of superconductivity in bilayer and trilayer
graphene, we theoretically investigate superconductivity and other interaction-driven
phases in multilayer graphene stacks. To this end, we study the density of states
of multilayer graphene with up to four layers at the single-particle band structure
level in the presence of a transverse electric field. Among the considered structures,
tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density
of states. We study the phases that can arise in ABCA graphene by tuning the carrier
density and transverse electric field. For a broad region of the tuning parameters,
the presence of strong Coulomb repulsion leads to a spontaneous spin and valley
symmetry breaking via Stoner transitions. Using a model that incorporates the
spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism
for superconductivity driven by repulsive Coulomb interactions. We find that the
strongest superconducting instability is in the p-wave channel, and occurs in
proximity to the onset of Stoner transitions. Interestingly, we find a range of
densities and transverse electric fields where superconductivity develops out
of a strongly corrugated, singly connected Fermi surface in each valley, leading
to a topologically nontrivial chiral p+ip superconducting state with an even number
of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked
tetralayer graphene as a promising platform for observing strongly correlated
physics and topological superconductivity.
acknowledgement: E.B. and T.H. were supported by the European Research Council (ERC)
under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science
Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.
article_number: '104502'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical
Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502
apa: Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes
as a platform for interaction-driven physics and topological superconductivity.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502
chicago: Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer
Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.
ieee: A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as
a platform for interaction-driven physics and topological superconductivity,”
Physical Review B, vol. 107, no. 10. American Physical Society, 2023.
ista: Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical Review
B. 107(10), 104502.
mla: Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven
Physics and Topological Superconductivity.” Physical Review B, vol. 107,
no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.
short: A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:59:29Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1103/PhysRevB.107.104502
external_id:
arxiv:
- '2211.02492'
isi:
- '000945526400003'
intvolume: ' 107'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.02492
month: '03'
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'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/
scopus_import: '1'
status: public
title: Multilayer graphenes as a platform for interaction-driven physics and topological
superconductivity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12791'
abstract:
- lang: eng
text: We investigate the capabilities of Physics-Informed Neural Networks (PINNs)
to reconstruct turbulent Rayleigh–Bénard flows using only temperature information.
We perform a quantitative analysis of the quality of the reconstructions at various
amounts of low-passed-filtered information and turbulent intensities. We compare
our results with those obtained via nudging, a classical equation-informed data
assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct
with high precision, comparable to the one achieved with nudging. At high Rayleigh
numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction
of the velocity fields only when data for temperature is provided with high spatial
and temporal density. When data becomes sparse, the PINNs performance worsens,
not only in a point-to-point error sense but also, and contrary to nudging, in
a statistical sense, as can be seen in the probability density functions and energy
spectra.
acknowledgement: This project has received partial funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(Grant Agreement No. 882340))
article_number: '16'
article_processing_charge: No
article_type: original
author:
- first_name: Patricio
full_name: Clark Di Leoni, Patricio
last_name: Clark Di Leoni
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Michele
full_name: Buzzicotti, Michele
last_name: Buzzicotti
- first_name: Luca
full_name: Biferale, Luca
last_name: Biferale
citation:
ama: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard
flows out of temperature-only measurements using Physics-Informed Neural Networks.
The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9
apa: Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023).
Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks. The European Physical Journal E. Springer
Nature. https://doi.org/10.1140/epje/s10189-023-00276-9
chicago: Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and
Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements
Using Physics-Informed Neural Networks.” The European Physical Journal E.
Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.
ieee: P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer
Nature, 2023.
ista: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks. The European Physical Journal E. 46(3), 16.
mla: Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out
of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The
European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.
short: P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European
Physical Journal E 46 (2023).
date_created: 2023-04-02T22:01:11Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-01T14:03:47Z
day: '20'
department:
- _id: CaMu
doi: 10.1140/epje/s10189-023-00276-9
external_id:
arxiv:
- '2301.07769'
isi:
- '000956387200001'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2301.07769'
month: '03'
oa: 1
oa_version: Preprint
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: Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 46
year: '2023'
...
---
_id: '12830'
abstract:
- lang: eng
text: Interstitial fluid (IF) accumulation between embryonic cells is thought to
be important for embryo patterning and morphogenesis. Here, we identify a positive
mechanical feedback loop between cell migration and IF relocalization and find
that it promotes embryonic axis formation during zebrafish gastrulation. We show
that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between
the yolk cell and deep cell tissue to extend the embryonic axis, compress the
overlying deep cell layer, thereby causing IF to flow from the deep cell layer
to the boundary between the yolk cell and the deep cell layer, directly ahead
of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion
formation and migration by opening up the space into which the ppl moves and,
thereby, the ability of the ppl to trigger IF relocalization by pushing against
the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic
feedback loop between cell migration and IF relocalization.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful
discussions and support with the SPIM experiments; the Heisenberg group, and especially
Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović
(ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and
zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia
Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura
(Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work
was supported by funding from the European Union (European Research Council Advanced
grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and
HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des
deutschen Volkes to F.P.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Friedrich
full_name: Preusser, Friedrich
last_name: Preusser
- first_name: Irene
full_name: Steccari, Irene
id: 2705C766-9FE2-11EA-B224-C6773DDC885E
last_name: Steccari
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop
between mesendoderm cell migration and interstitial fluid relocalization promotes
embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7.
doi:10.1016/j.devcel.2023.02.016
apa: Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I.,
Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between
mesendoderm cell migration and interstitial fluid relocalization promotes embryonic
axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016
chicago: Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser,
Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg.
“A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial
Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental
Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.
ieee: K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7,
2023.
ista: Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM,
Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish. Developmental Cell. 58(7), 582–596.e7.
mla: Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration
and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.”
Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.
short: K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M.
Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:10:38Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1016/j.devcel.2023.02.016
ec_funded: 1
external_id:
isi:
- '000982111800001'
file:
- access_level: open_access
checksum: c80ca2ebc241232aacdb5aa4b4c80957
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:41:25Z
date_updated: 2023-04-17T07:41:25Z
file_id: '12842'
file_name: 2023_DevelopmentalCell_Huljev.pdf
file_size: 7925886
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:41:25Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 582-596.e7
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 266BC5CE-B435-11E9-9278-68D0E5697425
grant_number: LT000429
name: Coordination of mesendoderm fate specification and internalization during
zebrafish gastrulation
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A hydraulic feedback loop between mesendoderm cell migration and interstitial
fluid relocalization promotes embryonic axis formation in zebrafish
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2023'
...
---
_id: '12831'
abstract:
- lang: eng
text: The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations
of a many-body bath, can be used to describe an impurity rotating in a fluid or
solid environment. Here, we propose a coherent state ansatz in the co-rotating
frame, which provides a comprehensive theoretical description of angulons. We
reveal the quasiparticle properties, such as energies, quasiparticle weights,
and spectral functions, and show that our ansatz yields a persistent decrease
in the impurity’s rotational constant due to many-body dressing, which is consistent
with experimental observations. From our study, a picture of the angulon emerges
as an effective spin interacting with a magnetic field that is self-consistently
generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy,
which focuses on the response of rotating molecules to a laser perturbation in
the linear response regime. Importantly, we take into account initial-state interactions
that have been neglected in prior studies and reveal their impact on the excitation
spectrum. To examine the angulon instability regime, we use a single-excitation
ansatz and obtain results consistent with experiments, in which a broadening of
spectral lines is observed while phonon wings remain highly suppressed due to
initial-state interactions.
acknowledgement: We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt
for their valuable discussions. We acknowledge support by the Max Planck Society
and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC
2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges
support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
T.S. is supported by the National Key Research and Development Program of China
(Grant No. 2017YFA0718304) and the National Natural Science Foundation of China
(Grant Nos. 11974363, 12135018, and 12047503).
article_number: '134301'
article_processing_charge: No
article_type: original
author:
- first_name: Zhongda
full_name: Zeng, Zhongda
last_name: Zeng
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Tao
full_name: Shi, Tao
last_name: Shi
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
citation:
ama: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons
and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13).
doi:10.1063/5.0135893
apa: Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational
theory of angulons and their rotational spectroscopy. The Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893
chicago: Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard
Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893.
ieee: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory
of angulons and their rotational spectroscopy,” The Journal of Chemical Physics,
vol. 158, no. 13. American Institute of Physics, 2023.
ista: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory
of angulons and their rotational spectroscopy. The Journal of Chemical Physics.
158(13), 134301.
mla: Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational
Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301,
American Institute of Physics, 2023, doi:10.1063/5.0135893.
short: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical
Physics 158 (2023).
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-07T00:00:00Z
date_updated: 2023-08-01T14:08:47Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0135893
ec_funded: 1
external_id:
arxiv:
- '2211.08070'
isi:
- '000970038800001'
file:
- access_level: open_access
checksum: 8d801babea4df48e08895c76571bb19e
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:28:38Z
date_updated: 2023-04-17T07:28:38Z
file_id: '12841'
file_name: 2023_JourChemicalPhysics_Zeng.pdf
file_size: 7388057
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:28:38Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '13'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variational theory of angulons and their rotational spectroscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2023'
...
---
_id: '12839'
abstract:
- lang: eng
text: Universal nonequilibrium properties of isolated quantum systems are typically
probed by studying transport of conserved quantities, such as charge or spin,
while transport of energy has received considerably less attention. Here, we study
infinite-temperature energy transport in the kinetically constrained PXP model
describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations,
including exact diagonalization and time-evolving block decimation methods, reveal
the existence of two distinct transport regimes. At moderate times, the energy-energy
correlation function displays periodic oscillations due to families of eigenstates
forming different su(2) representations hidden within the spectrum. These families
of eigenstates generalize the quantum many-body scarred states found in previous
works and leave an imprint on the infinite-temperature energy transport. At later
times, we observe a long-lived superdiffusive transport regime that we attribute
to the proximity of a nearby integrable point. While generic strong deformations
of the PXP model indeed restore diffusive transport, adding a strong chemical
potential intriguingly gives rise to a well-converged superdiffusive exponent
z≈3/2. Our results suggest constrained models to be potential hosts of novel transport
regimes and call for developing an analytic understanding of their energy transport.
acknowledgement: "We would like to thank Alexios Michailidis, Sarang Gopalakrishnan,
and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support
by the European Research Council under the European Union’s Horizon 2020 research
and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge
support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership
Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research
data: This publication is theoretical work that does not require supporting research
data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International
Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for
awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations
were performed. The TEBD\r\nsimulations were performed using the ITENSOR library
[54]."
article_number: '011033'
article_processing_charge: No
article_type: original
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Jean Yves
full_name: Desaules, Jean Yves
last_name: Desaules
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033
apa: Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive
energy transport in kinetically constrained models. Physical Review X.
American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033
chicago: Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić.
“Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical
Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.
ieee: M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy
transport in kinetically constrained models,” Physical Review X, vol. 13,
no. 1. American Physical Society, 2023.
ista: Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 13(1), 011033.
mla: Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained
Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society,
2023, doi:10.1103/PhysRevX.13.011033.
short: M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).
date_created: 2023-04-16T22:01:09Z
date_published: 2023-03-07T00:00:00Z
date_updated: 2023-08-01T14:11:28Z
day: '07'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevX.13.011033
ec_funded: 1
external_id:
isi:
- '000957625700001'
file:
- access_level: open_access
checksum: ee060cea609af79bba7af74b1ce28078
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T08:36:53Z
date_updated: 2023-04-17T08:36:53Z
file_id: '12845'
file_name: 2023_PhysReviewX_Ljubotina.pdf
file_size: 1958523
relation: main_file
success: 1
file_date_updated: 2023-04-17T08:36:53Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superdiffusive energy transport in kinetically constrained models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '12822'
abstract:
- lang: eng
text: Gears and cogwheels are elemental components of machines. They restrain degrees
of freedom and channel power into a specified motion. Building and powering small-scale
cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy
injection, and control are, however, a challenge at the microscale. In contrast
with passive gears, whose function is to transmit torques from one to another,
interlocking and untethered active gears have the potential to unveil dynamics
and functions untapped by externally driven mechanisms. Here, it is shown the
assembly and control of a family of self-spinning cogwheels with varying teeth
numbers and study the interlocking of multiple cogwheels. The teeth are formed
by colloidal microswimmers that power the structure. The cogwheels are autonomous
and active, showing persistent rotation. Leveraging the angular momentum of optical
vortices, we control the direction of rotation of the cogwheels. The pairs of
interlocking and active cogwheels that roll over each other in a random walk and
have curvature-dependent mobility are studied. This behavior is leveraged to self-position
parts and program microbots, demonstrating the ability to pick up, direct, and
release a load. The work constitutes a step toward autonomous machinery with external
control as well as (re)programmable microbots and matter.
acknowledgement: 'Army Research Office. Grant Number: W911NF-20-1-0112'
article_number: '2200129'
article_processing_charge: No
article_type: original
author:
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning
of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129
apa: Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking,
and self‐positioning of active cogwheels. Advanced Intelligent Systems.
Wiley. https://doi.org/10.1002/aisy.202200129
chicago: Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control,
Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent
Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129.
ieee: Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking,
and self‐positioning of active cogwheels,” Advanced Intelligent Systems,
vol. 5, no. 1. Wiley, 2023.
ista: Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and
self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.
mla: Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning
of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129,
Wiley, 2023, doi:10.1002/aisy.202200129.
short: Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).
date_created: 2023-04-12T08:30:03Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T14:06:50Z
day: '01'
ddc:
- '530'
department:
- _id: JePa
doi: 10.1002/aisy.202200129
external_id:
arxiv:
- '2201.03333'
isi:
- '000852291200001'
file:
- access_level: open_access
checksum: d48fc41d39892e7fa0d44cb352dd46aa
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T06:44:17Z
date_updated: 2023-04-17T06:44:17Z
file_id: '12840'
file_name: 2023_AdvancedIntelligentSystems_Martinet.pdf
file_size: 2414125
relation: main_file
success: 1
file_date_updated: 2023-04-17T06:44:17Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Advanced Intelligent Systems
publication_identifier:
issn:
- 2640-4567
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Rotation control, interlocking, and self‐positioning of active cogwheels
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '12818'
abstract:
- lang: eng
text: The multicellular organization of diverse systems, including embryos, intestines,
and tumors relies on coordinated cell migration in curved environments. In these
settings, cells establish supracellular patterns of motion, including collective
rotation and invasion. While such collective modes have been studied extensively
in flat systems, the consequences of geometrical and topological constraints on
collective migration in curved systems are largely unknown. Here, we discover
a collective mode of cell migration in rotating spherical tissues manifesting
as a propagating single-wavelength velocity wave. This wave is accompanied by
an apparently incompressible supracellular flow pattern featuring topological
defects as dictated by the spherical topology. Using a minimal active particle
model, we reveal that this collective mode arises from the effect of curvature
on the active flocking behavior of a cell layer confined to a spherical surface.
Our results thus identify curvature-induced velocity waves as a mode of collective
cell migration, impacting the dynamical organization of 3D curved tissues.
acknowledgement: We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti,
and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B.
is a NOMIS fellow supported by the NOMIS foundation and was in part supported by
a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM)
and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science
Program (LT000475/2018-C) and from the National Science Foundation, through the
Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support
from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open
Access funding enabled and organized by Projekt DEAL.
article_number: '1643'
article_processing_charge: No
article_type: original
author:
- first_name: Tom
full_name: Brandstätter, Tom
last_name: Brandstätter
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Yu Long
full_name: Han, Yu Long
last_name: Han
- first_name: Ricard
full_name: Alert, Ricard
last_name: Alert
- first_name: Ming
full_name: Guo, Ming
last_name: Guo
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
2023;14. doi:10.1038/s41467-023-37054-2
apa: Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz,
C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2
chicago: Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo,
and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical
Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.
ieee: T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz,
“Curvature induces active velocity waves in rotating spherical tissues,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
14, 1643.
mla: Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating
Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature,
2023, doi:10.1038/s41467-023-37054-2.
short: T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz,
Nature Communications 14 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-24T00:00:00Z
date_updated: 2023-08-01T14:05:30Z
day: '24'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-023-37054-2
external_id:
isi:
- '000959887700008'
pmid:
- '36964141'
file:
- access_level: open_access
checksum: 54f06f9eee11d43bab253f3492c983ba
content_type: application/pdf
creator: dernst
date_created: 2023-04-11T06:27:00Z
date_updated: 2023-04-11T06:27:00Z
file_id: '12821'
file_name: 2023_NatureComm_Brandstaetter.pdf
file_size: 4146777
relation: main_file
success: 1
file_date_updated: 2023-04-11T06:27:00Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature induces active velocity waves in rotating spherical tissues
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12819'
abstract:
- lang: eng
text: 'Reaching a high cavity population with a coherent pump in the strong-coupling
regime of a single-atom laser is impossible due to the photon blockade effect.
In this Letter, we experimentally demonstrate that in a single-atom maser based
on a transmon strongly coupled to two resonators, it is possible to pump over
a dozen photons into the system. The first high-quality resonator plays the role
of a usual lasing cavity, and the second one presents a controlled dissipation
channel, bolstering population inversion, and modifies the energy-level structure
to lift the blockade. As confirmation of the lasing action, we observe conventional
laser features such as a narrowing of the emission linewidth and external signal
amplification. Additionally, we report unique single-atom features: self-quenching
and several lasing thresholds.'
acknowledgement: We thank N.N. Abramov for assistance with the experimental setup.
The sample was fabricated using equipment of MIPT Shared Facilities Center. This
research was supported by Russian Science Foundation, grant no. 21-72-30026.
article_number: L031701
article_processing_charge: No
article_type: letter_note
author:
- first_name: Alesya
full_name: Sokolova, Alesya
id: 2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a
last_name: Sokolova
orcid: 0000-0002-8308-4144
- first_name: D. A.
full_name: Kalacheva, D. A.
last_name: Kalacheva
- first_name: G. P.
full_name: Fedorov, G. P.
last_name: Fedorov
- first_name: O. V.
full_name: Astafiev, O. V.
last_name: Astafiev
citation:
ama: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade
in a circuit-QED single-atom maser with engineered metastability and strong coupling.
Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701
apa: Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023).
Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.107.L031701
chicago: Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming
Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability
and Strong Coupling.” Physical Review A. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevA.107.L031701.
ieee: A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming
photon blockade in a circuit-QED single-atom maser with engineered metastability
and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical
Society, 2023.
ista: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon
blockade in a circuit-QED single-atom maser with engineered metastability and
strong coupling. Physical Review A. 107(3), L031701.
mla: Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom
Maser with Engineered Metastability and Strong Coupling.” Physical Review A,
vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.
short: A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review
A 107 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-22T00:00:00Z
date_updated: 2023-08-01T14:06:05Z
day: '22'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.107.L031701
external_id:
arxiv:
- '2209.05165'
isi:
- '000957799000006'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2209.05165
month: '03'
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: Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12861'
abstract:
- lang: eng
text: The field of indirect reciprocity investigates how social norms can foster
cooperation when individuals continuously monitor and assess each other’s social
interactions. By adhering to certain social norms, cooperating individuals can
improve their reputation and, in turn, receive benefits from others. Eight social
norms, known as the “leading eight," have been shown to effectively promote the
evolution of cooperation as long as information is public and reliable. These
norms categorize group members as either ’good’ or ’bad’. In this study, we examine
a scenario where individuals instead assign nuanced reputation scores to each
other, and only cooperate with those whose reputation exceeds a certain threshold.
We find both analytically and through simulations that such quantitative assessments
are error-correcting, thus facilitating cooperation in situations where information
is private and unreliable. Moreover, our results identify four specific norms
that are robust to such conditions, and may be relevant for helping to sustain
cooperation in natural populations.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support
by the Stochastic Analysis and Application Research Center (SAARC) under National
Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally
thank Stefan Schmid for providing access to his lab infrastructure at the University
of Vienna for the purpose of collecting simulation data.'
article_number: '2086'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Farbod
full_name: Ekbatani, Farbod
last_name: Ekbatani
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize
indirect reciprocity under imperfect information. Nature Communications.
2023;14. doi:10.1038/s41467-023-37817-x
apa: Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative
assessment can stabilize indirect reciprocity under imperfect information. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x
chicago: Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee.
“Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.
ieee: L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment
can stabilize indirect reciprocity under imperfect information,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment
can stabilize indirect reciprocity under imperfect information. Nature Communications.
14, 2086.
mla: Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity
under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer
Nature, 2023, doi:10.1038/s41467-023-37817-x.
short: L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14
(2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2023-08-01T14:15:57Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-37817-x
ec_funded: 1
external_id:
isi:
- '001003644100020'
pmid:
- '37045828'
file:
- access_level: open_access
checksum: a4b3b7b36fbef068cabf4fb99501fef6
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T09:13:53Z
date_updated: 2023-04-25T09:13:53Z
file_id: '12868'
file_name: 2023_NatureComm_Schmid.pdf
file_size: 1786475
relation: main_file
success: 1
file_date_updated: 2023-04-25T09:13:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative assessment can stabilize indirect reciprocity under imperfect
information
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12862'
abstract:
- lang: eng
text: Despite the considerable progress of in vivo neural recording techniques,
inferring the biophysical mechanisms underlying large scale coordination of brain
activity from neural data remains challenging. One obstacle is the difficulty
to link high dimensional functional connectivity measures to mechanistic models
of network activity. We address this issue by investigating spike-field coupling
(SFC) measurements, which quantify the synchronization between, on the one hand,
the action potentials produced by neurons, and on the other hand mesoscopic “field”
signals, reflecting subthreshold activities at possibly multiple recording sites.
As the number of recording sites gets large, the amount of pairwise SFC measurements
becomes overwhelmingly challenging to interpret. We develop Generalized Phase
Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate
SFC. GPLA describes the dominant coupling between field activity and neural ensembles
across space and frequencies. We show that GPLA features are biophysically interpretable
when used in conjunction with appropriate network models, such that we can identify
the influence of underlying circuit properties on these features. We demonstrate
the statistical benefits and interpretability of this approach in various computational
models and Utah array recordings. The results suggest that GPLA, used jointly
with biophysical modeling, can help uncover the contribution of recurrent microcircuits
to the spatio-temporal dynamics observed in multi-channel experimental recordings.
acknowledgement: "We thank Britni Crocker for help with preprocessing of the data
and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support;
Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll
authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal
Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe
Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from
the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02).
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript. "
article_number: e1010983
article_processing_charge: No
article_type: original
author:
- first_name: Shervin
full_name: Safavi, Shervin
last_name: Safavi
- first_name: Theofanis I.
full_name: Panagiotaropoulos, Theofanis I.
last_name: Panagiotaropoulos
- first_name: Vishal
full_name: Kapoor, Vishal
last_name: Kapoor
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
citation:
ama: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK,
Besserve M. Uncovering the organization of neural circuits with Generalized Phase
Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983
apa: Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F.,
Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural
circuits with Generalized Phase Locking Analysis. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983
chicago: Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F
Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization
of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational
Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.
ieee: S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N.
K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits
with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol.
19, no. 4. Public Library of Science, 2023.
ista: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis
NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized
Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.
mla: Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with
Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19,
no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.
short: S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K.
Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-01T14:15:16Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pcbi.1010983
external_id:
isi:
- '000962668700002'
file:
- access_level: open_access
checksum: edeb9d09f3e41ba7c0251308b9e372e7
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T08:59:18Z
date_updated: 2023-04-25T08:59:18Z
file_id: '12867'
file_name: 2023_PLoSCompBio_Safavi.pdf
file_size: 4737671
relation: main_file
success: 1
file_date_updated: 2023-04-25T08:59:18Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/shervinsafavi/gpla.git
scopus_import: '1'
status: public
title: Uncovering the organization of neural circuits with Generalized Phase Locking
Analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '12879'
abstract:
- lang: eng
text: Machine learning (ML) has been widely applied to chemical property prediction,
most prominently for the energies and forces in molecules and materials. The strong
interest in predicting energies in particular has led to a ‘local energy’-based
paradigm for modern atomistic ML models, which ensures size-extensivity and a
linear scaling of computational cost with system size. However, many electronic
properties (such as excitation energies or ionization energies) do not necessarily
scale linearly with system size and may even be spatially localized. Using size-extensive
models in these cases can lead to large errors. In this work, we explore different
strategies for learning intensive and localized properties, using HOMO energies
in organic molecules as a representative test case. In particular, we analyze
the pooling functions that atomistic neural networks use to predict molecular
properties, and suggest an orbital weighted average (OWA) approach that enables
the accurate prediction of orbital energies and locations.
acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is
grateful for the TUM graduate school finance support to visit Bingqing Cheng's group
in IST for two months. We also thankfully acknowledge computational resources provided
by the MPCDF Supercomputing Centre.
article_processing_charge: No
article_type: original
author:
- first_name: Ke
full_name: Chen, Ke
id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d
last_name: Chen
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
citation:
ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning
of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j
apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired
machine learning of localized intensive properties. Chemical Science. Royal
Society of Chemistry. https://doi.org/10.1039/d3sc00841j
chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes
T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.”
Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.
ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired
machine learning of localized intensive properties,” Chemical Science.
Royal Society of Chemistry, 2023.
ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine
learning of localized intensive properties. Chemical Science.
mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive
Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.
short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:18:10Z
day: '10'
ddc:
- '000'
- '540'
department:
- _id: BiCh
doi: 10.1039/d3sc00841j
external_id:
isi:
- '000971508100001'
file:
- access_level: open_access
checksum: 5eeec69a51e192dcd94b955d84423836
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:17:05Z
date_updated: 2023-05-02T07:17:05Z
file_id: '12883'
file_name: 2023_ChemialScience_Chen.pdf
file_size: 1515446
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:17:05Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics-inspired machine learning of localized intensive properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12876'
abstract:
- lang: eng
text: "Motivation: The problem of model inference is of fundamental importance to
systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally
attractive approach capable of handling large biological networks. The models
are typically inferred from experimental data. However, even with a substantial
amount of experimental data supported by some prior knowledge, existing inference
methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults:
We propose Boolean network sketches as a new formal instrument for the inference
of Boolean networks. A sketch integrates (typically partial) knowledge about the
network’s topology and the update logic (obtained through, e.g. a biological knowledge
base or a literature search), as well as further assumptions about the properties
of the network’s transitions (e.g. the form of its attractor landscape), and additional
restrictions on the model dynamics given by the measured experimental data. Our
new BNs inference algorithm starts with an ‘initial’ sketch, which is extended
by adding restrictions representing experimental data to a ‘data-informed’ sketch
and subsequently computes all BNs consistent with the data-informed sketch. Our
algorithm is based on a symbolic representation and coloured model-checking. Our
approach is unique in its ability to cover a broad spectrum of knowledge and efficiently
produce a compact representation of all inferred BNs. We evaluate the method on
a non-trivial collection of real-world and simulated data."
acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S];
and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was
partially supported by European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].
article_number: btad158
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Ondřej
full_name: Huvar, Ondřej
last_name: Huvar
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
citation:
ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 2023;39(4).
doi:10.1093/bioinformatics/btad158'
apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean
network sketches: A unifying framework for logical model inference. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158'
chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek.
“Boolean Network Sketches: A Unifying Framework for Logical Model Inference.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.'
ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network
sketches: A unifying framework for logical model inference,” Bioinformatics,
vol. 39, no. 4. Oxford Academic, 2023.'
ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.'
mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for
Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford
Academic, 2023, doi:10.1093/bioinformatics/btad158.'
short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).
date_created: 2023-04-30T22:01:05Z
date_published: 2023-04-03T00:00:00Z
date_updated: 2023-08-01T14:27:28Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad158
ec_funded: 1
external_id:
isi:
- '000976610800001'
pmid:
- '37004199'
file:
- access_level: open_access
checksum: 2cb90ddf781baefddf47eac4b54e2a03
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:39:04Z
date_updated: 2023-05-02T07:39:04Z
file_id: '12886'
file_name: 2023_Bioinformatics_Benes.pdf
file_size: 478740
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:39:04Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.7688740
scopus_import: '1'
status: public
title: 'Boolean network sketches: A unifying framework for logical model inference'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2023'
...
---
_id: '12880'
abstract:
- lang: eng
text: Peripheral heterochromatin positioning depends on nuclear envelope associated
proteins and repressive histone modifications. Here we show that overexpression
(OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin
into heterochromatic foci within the nucleoplasm. These changes represent a perturbation
of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent
from altering other heterochromatin anchors or histone post-translational modifications.
We further show that LmnB1 OE alters gene expression. These changes do not correlate
with different levels of H3K9me3, but a significant number of the misregulated
genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed
an enrichment of developmental processes amongst the upregulated genes. ~74% of
these genes were normally repressed in our cell type, suggesting that LmnB1 OE
promotes gene de-repression. This demonstrates a broader consequence of LmnB1
OE on cell fate, and highlights the importance of maintaining proper levels of
LmnB1.
acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript;
Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing
Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195,
the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run
libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute,
with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg
Initiative Imaging Scientist Award, for electron microscopy sample preparation and
imaging.'
article_number: '2202548'
article_processing_charge: No
article_type: original
author:
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin
organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548
apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression
alters chromatin organization and gene expression. Nucleus. Taylor &
Francis. https://doi.org/10.1080/19491034.2023.2202548
chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1
Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus.
Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.
ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression
alters chromatin organization and gene expression,” Nucleus, vol. 14, no.
1. Taylor & Francis, 2023.
ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters
chromatin organization and gene expression. Nucleus. 14(1), 2202548.
mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization
and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis,
2023, doi:10.1080/19491034.2023.2202548.
short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:18:46Z
day: '18'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1080/19491034.2023.2202548
external_id:
isi:
- '000971629400001'
pmid:
- '37071033'
file:
- access_level: open_access
checksum: 8e707eda84f64dbad7f03545ae0a83ef
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:24:55Z
date_updated: 2023-05-02T07:24:55Z
file_id: '12884'
file_name: 2023_Nucleus_Kaneshiro.pdf
file_size: 3811113
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:24:55Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleus
publication_identifier:
eissn:
- 1949-1042
issn:
- 1949-1034
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamin B1 overexpression alters chromatin organization and gene expression
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12914'
abstract:
- lang: eng
text: We numerically study two methods of measuring tunneling times using a quantum
clock. In the conventional method using the Larmor clock, we show that the Larmor
tunneling time can be shorter for higher tunneling barriers. In the second method,
we study the probability of a spin-flip of a particle when it is transmitted through
a potential barrier including a spatially rotating field interacting with its
spin. According to the adiabatic theorem, the probability depends on the velocity
of the particle inside the barrier. It is numerically observed that the probability
increases for higher barriers, which is consistent with the result obtained by
the Larmor clock. By comparing outcomes for different initial spin states, we
suggest that one of the main causes of the apparent decrease in the tunneling
time can be the filtering effect occurring at the end of the barrier.
acknowledgement: We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C.
H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos
National Laboratory LDRD program under Project No. 20230049DR and the Center for
Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and
innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support.
W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the
Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support
while this work was being done.
article_number: '042216'
article_processing_charge: No
article_type: original
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: William G.
full_name: Unruh, William G.
last_name: Unruh
citation:
ama: Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling
times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216
apa: Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations
for measuring tunneling times. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.107.042216
chicago: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A. American Physical Society,
2023. https://doi.org/10.1103/PhysRevA.107.042216.
ieee: F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring
tunneling times,” Physical Review A, vol. 107, no. 4. American Physical
Society, 2023.
ista: Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring
tunneling times. Physical Review A. 107(4), 042216.
mla: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216,
American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.
short: F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-08-01T14:33:21Z
day: '20'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.107.042216
ec_funded: 1
external_id:
arxiv:
- '2207.13130'
isi:
- '000975799300006'
intvolume: ' 107'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2207.13130
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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: Numerical quantum clock simulations for measuring tunneling times
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12913'
abstract:
- lang: eng
text: The coexistence of gate-tunable superconducting, magnetic and topological
orders in magic-angle twisted bilayer graphene provides opportunities for the
creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined
symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where
the weak link is gate-tuned close to the correlated insulator state with a moiré
filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer
pattern with a pronounced magnetic hysteresis. Our theoretical calculations of
the junction weak link—with valley polarization and orbital magnetization—explain
most of these unconventional features. The effects persist up to the critical
temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show
how the combination of magnetization and its current-induced magnetization switching
allows us to realise a programmable zero-field superconducting diode. Our results
represent a major advance towards the creation of future superconducting quantum
electronic devices.
acknowledgement: We are grateful for the fruitful discussions with Allan MacDonald
and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and
Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence
in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat
de Catalunya through the CERCA program, funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support
of the Ministry of Science and Technology of China and the HKRGC through grants
MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support
from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021).
Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.
article_number: '2396'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Díez-Mérida, J.
last_name: Díez-Mérida
- first_name: A.
full_name: Díez-Carlón, A.
last_name: Díez-Carlón
- first_name: S. Y.
full_name: Yang, S. Y.
last_name: Yang
- first_name: Y. M.
full_name: Xie, Y. M.
last_name: Xie
- first_name: X. J.
full_name: Gao, X. J.
last_name: Gao
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: X.
full_name: Lu, X.
last_name: Lu
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: K. T.
full_name: Law, K. T.
last_name: Law
- first_name: Dmitri K.
full_name: Efetov, Dmitri K.
last_name: Efetov
citation:
ama: Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions
and superconducting diodes in magic-angle twisted bilayer graphene. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38005-7
apa: Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior,
J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-38005-7
chicago: Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden
L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.
ieee: J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe
K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken
Josephson junctions and superconducting diodes in magic-angle twisted bilayer
graphene. Nature Communications. 14, 2396.
mla: Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications,
vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.
short: J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior,
K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature
Communications 14 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-08-01T14:34:00Z
day: '26'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.1038/s41467-023-38005-7
external_id:
isi:
- '000979744000004'
pmid:
- '37100775'
file:
- access_level: open_access
checksum: a778105665c10beb2354c92d2b295115
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:26:40Z
date_updated: 2023-05-08T07:26:40Z
file_id: '12917'
file_name: 2023_NatureComm_DiezMerida.pdf
file_size: 1405588
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:26:40Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-broken Josephson junctions and superconducting diodes in magic-angle
twisted bilayer graphene
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '10550'
abstract:
- lang: eng
text: The global existence of renormalised solutions and convergence to equilibrium
for reaction-diffusion systems with non-linear diffusion are investigated. The
system is assumed to have quasi-positive non-linearities and to satisfy an entropy
inequality. The difficulties in establishing global renormalised solutions caused
by possibly degenerate diffusion are overcome by introducing a new class of weighted
truncation functions. By means of the obtained global renormalised solutions,
we study the large-time behaviour of complex balanced systems arising from chemical
reaction network theory with non-linear diffusion. When the reaction network does
not admit boundary equilibria, the complex balanced equilibrium is shown, by using
the entropy method, to exponentially attract all renormalised solutions in the
same compatibility class. This convergence extends even to a range of non-linear
diffusion, where global existence is an open problem, yet we are able to show
that solutions to approximate systems converge exponentially to equilibrium uniformly
in the regularisation parameter.
acknowledgement: "We thank the referees for their valuable comments and suggestions.
A major part of this work was carried out when B. Q. Tang visited the Institute
of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged.
This work was partially supported by NAWI Graz.\r\nOpen access funding provided
by University of Graz."
article_number: '66'
article_processing_charge: No
article_type: original
author:
- first_name: Klemens
full_name: Fellner, Klemens
last_name: Fellner
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
- first_name: Bao Quoc
full_name: Tang, Bao Quoc
last_name: Tang
citation:
ama: Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and
equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w
apa: Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion.
Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w
chicago: Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang.
“Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems
with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature,
2023. https://doi.org/10.1007/s00332-023-09926-w.
ieee: K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion,”
Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.
ista: Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions
and equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 33, 66.
mla: Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of
Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear
Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.
short: K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science
33 (2023).
date_created: 2021-12-16T12:15:35Z
date_published: 2023-06-07T00:00:00Z
date_updated: 2023-08-01T14:40:33Z
day: '07'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00332-023-09926-w
external_id:
arxiv:
- '2109.12019'
isi:
- '001002343400002'
file:
- access_level: open_access
checksum: f3f0f0886098e31c81116cff8183750b
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T07:33:53Z
date_updated: 2023-06-19T07:33:53Z
file_id: '13149'
file_name: 2023_JourNonlinearScience_Fellner.pdf
file_size: 742315
relation: main_file
success: 1
file_date_updated: 2023-06-19T07:33:53Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Journal of Nonlinear Science
publication_identifier:
eissn:
- 1432-1467
issn:
- 0938-8974
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global renormalised solutions and equilibration of reaction-diffusion systems
with non-linear diffusion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2023'
...
---
_id: '13043'
abstract:
- lang: eng
text: "We derive a weak-strong uniqueness principle for BV solutions to multiphase
mean curvature flow of triple line clusters in three dimensions. Our proof is
based on the explicit construction\r\nof a gradient flow calibration in the sense
of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends
the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting
along triple junctions."
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. 948819), and from the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Tim
full_name: Laux, Tim
last_name: Laux
citation:
ama: Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double
bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484
apa: Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature
flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484
chicago: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature
Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023.
https://doi.org/10.4171/IFB/484.
ieee: S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow
of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS
Press, pp. 37–107, 2023.
ista: Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow
of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.
mla: Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature
Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1,
EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.
short: S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.
date_created: 2023-05-21T22:01:06Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-08-01T14:43:29Z
day: '20'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.4171/IFB/484
ec_funded: 1
external_id:
arxiv:
- '2108.01733'
isi:
- '000975817300002'
file:
- access_level: open_access
checksum: 622422484810441e48f613e968c7e7a4
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:24:13Z
date_updated: 2023-05-22T07:24:13Z
file_id: '13045'
file_name: 2023_Interfaces_Hensel.pdf
file_size: 867876
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:24:13Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 37-107
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Interfaces and Free Boundaries
publication_identifier:
eissn:
- 1463-9971
issn:
- 1463-9963
publication_status: published
publisher: EMS Press
quality_controlled: '1'
related_material:
record:
- id: '10013'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Weak-strong uniqueness for the mean curvature flow of double bubbles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2023'
...
---
_id: '12912'
abstract:
- lang: eng
text: The chemical potential of adsorbed or confined fluids provides insight into
their unique thermodynamic properties and determines adsorption isotherms. However,
it is often difficult to compute this quantity from atomistic simulations using
existing statistical mechanical methods. We introduce a computational framework
that utilizes static structure factors, thermodynamic integration, and free energy
perturbation for calculating the absolute chemical potential of fluids. For demonstration,
we apply the method to compute the adsorption isotherms of carbon dioxide in a
metal-organic framework and water in carbon nanotubes.
acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments
and suggestions on the article. B.C. acknowledges the 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.
article_number: '161101 '
article_processing_charge: No
article_type: original
author:
- first_name: Rochus
full_name: Schmid, Rochus
last_name: Schmid
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids.
The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711
apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed
or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711
chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023.
https://doi.org/10.1063/5.0146711.
ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined
fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing,
2023.
ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined
fluids. The Journal of Chemical Physics. 158(16), 161101.
mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16,
161101, AIP Publishing, 2023, doi:10.1063/5.0146711.
short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-24T00:00:00Z
date_updated: 2023-08-01T14:34:49Z
day: '24'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0146711
external_id:
arxiv:
- '2302.01297'
isi:
- '001010676000010'
pmid:
- '37093149'
file:
- access_level: open_access
checksum: 4ab8c965f2fa4e17920bfa846847f137
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:44:49Z
date_updated: 2023-05-08T07:44:49Z
file_id: '12918'
file_name: 2023_JourChemicalPhysics_Schmid.pdf
file_size: 6499468
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:44:49Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/mu-adsorption
- relation: software
url: https://github.com/BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of adsorbed or confined fluids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2023'
...
---
_id: '12972'
abstract:
- lang: eng
text: Embroidery is a long-standing and high-quality approach to making logos and
images on textiles. Nowadays, it can also be performed via automated machines
that weave threads with high spatial accuracy. A characteristic feature of the
appearance of the threads is a high degree of anisotropy. The anisotropic behavior
is caused by depositing thin but long strings of thread. As a result, the stitched
patterns convey both color and direction. Artists leverage this anisotropic behavior
to enhance pure color images with textures, illusions of motion, or depth cues.
However, designing colorful embroidery patterns with prescribed directionality
is a challenging task, one usually requiring an expert designer. In this work,
we propose an interactive algorithm that generates machine-fabricable embroidery
patterns from multi-chromatic images equipped with user-specified directionality
fields.We cast the problem of finding a stitching pattern into vector theory.
To find a suitable stitching pattern, we extract sources and sinks from the divergence
field of the vector field extracted from the input and use them to trace streamlines.
We further optimize the streamlines to guarantee a smooth and connected stitching
pattern. The generated patterns approximate the color distribution constrained
by the directionality field. To allow for further artistic control, the trade-off
between color match and directionality match can be interactively explored via
an intuitive slider. We showcase our approach by fabricating several embroidery
paths.
acknowledgement: This work was supported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program (grant agreement
No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous
reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and
Paola Mejia for proofreading; everyone in the visual computing group at ISTA for
inspiring lunch and coffee breaks; Thibault Tricard for help producing the results
of Phasor Noise.
article_processing_charge: No
article_type: original
author:
- first_name: Zhenyuan
full_name: Liu, Zhenyuan
id: 70f0d7cf-ae65-11ec-a14f-89dfc5505b19
last_name: Liu
orcid: 0000-0001-9200-5690
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Raphael
full_name: Charrondiere, Raphael
id: a3a24133-2cc7-11ec-be88-8ddaf6f464b1
last_name: Charrondiere
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware
design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409.
doi:10.1111/cgf.14770
apa: 'Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023).
Directionality-aware design of embroidery patterns. Computer Graphics Forum.
Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770
'
chicago: Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere,
and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer
Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770
.
ieee: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware
design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2.
Wiley, pp. 397–409, 2023.
ista: Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware
design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409.
mla: Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.”
Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .
short: Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics
Forum 42 (2023) 397–409.
conference:
end_date: 2023-05-12
location: Saarbrucken, Germany
name: 'EG: Eurographics'
start_date: 2023-05-08
date_created: 2023-05-16T08:47:25Z
date_published: 2023-05-08T00:00:00Z
date_updated: 2023-08-01T14:47:05Z
day: '08'
ddc:
- '004'
department:
- _id: BeBi
doi: '10.1111/cgf.14770 '
ec_funded: 1
external_id:
isi:
- '001000062600033'
file:
- access_level: open_access
checksum: 4c188c2be4745467a8790bbf5d6491aa
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T08:28:37Z
date_updated: 2023-05-16T08:28:37Z
file_id: '12974'
file_name: Zhenyuan2023.pdf
file_size: 24003702
relation: main_file
success: 1
file_date_updated: 2023-05-16T08:28:37Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '2'
keyword:
- embroidery
- design
- directionality
- density
- image
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 397-409
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics Forum
publication_identifier:
issn:
- 1467-8659
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Directionality-aware design of embroidery patterns
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 42
year: '2023'
...
---
_id: '13033'
abstract:
- lang: eng
text: Current methods for assessing cell proliferation in 3D scaffolds rely on changes
in metabolic activity or total DNA, however, direct quantification of cell number
in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased
stereology approach that uses systematic-random sampling and thin focal-plane
optical sectioning of the scaffolds followed by estimation of total cell number
(StereoCount). This approach was validated against an indirect method for measuring
the total DNA (DNA content); and the Bürker counting chamber, the current reference
method for quantifying cell number. We assessed the total cell number for cell
seeding density (cells per unit volume) across four values and compared the methods
in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount
markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold.
For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA
content showed lower accuracy than the Bürker but did not differ from each other.
In terms of ease-of-use, there was a strong advantage for the StereoCount due
to output in terms of absolute cell numbers along with the possibility for an
overview of cell distribution and future use of automation for high throughput
analysis. Taking together, the StereoCount method is an efficient approach for
direct cell quantification in 3D collagen scaffolds. Its major benefit is that
automated StereoCount could accelerate research using 3D scaffolds focused on
drug discovery for a wide variety of human diseases.
acknowledgement: The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787
“Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the
Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE
project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein
and Norway through the EEA Grants and the Technology Agency of the Czech Republic
and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation
(U.S. Public Health Service). The authors acknowledge the invaluable assistance
provided by Iveta Paurova via her support in terms of the provision of laboratory
services.
article_number: '7959'
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Zavadakova, Anna
last_name: Zavadakova
- first_name: Lucie
full_name: Vistejnova, Lucie
last_name: Vistejnova
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Filip
full_name: Tichanek, Filip
last_name: Tichanek
- first_name: Dagmar
full_name: Bilikova, Dagmar
last_name: Bilikova
- first_name: Peter R.
full_name: Mouton, Peter R.
last_name: Mouton
citation:
ama: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
Novel stereological method for estimation of cell counts in 3D collagen scaffolds.
Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z
apa: Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &
Mouton, P. R. (2023). Novel stereological method for estimation of cell counts
in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z
chicago: Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar
Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature,
2023. https://doi.org/10.1038/s41598-023-35162-z.
ieee: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P.
R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen
scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.
ista: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
2023. Novel stereological method for estimation of cell counts in 3D collagen
scaffolds. Scientific Reports. 13(1), 7959.
mla: Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959,
Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.
short: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R.
Mouton, Scientific Reports 13 (2023).
date_created: 2023-05-19T11:12:25Z
date_published: 2023-05-17T00:00:00Z
date_updated: 2023-08-01T14:46:06Z
day: '17'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1038/s41598-023-35162-z
external_id:
isi:
- '000995271600104'
file:
- access_level: open_access
checksum: 8c1b769693ff4288df8376e59ad1176d
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:57:37Z
date_updated: 2023-05-22T07:57:37Z
file_id: '13047'
file_name: 2023_ScientificReports_Zavadakova.pdf
file_size: 3055077
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:57:37Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41598-023-37265-z
scopus_import: '1'
status: public
title: Novel stereological method for estimation of cell counts in 3D collagen scaffolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '13095'
abstract:
- lang: eng
text: Disulfide bond formation is fundamentally important for protein structure
and constitutes a key mechanism by which cells regulate the intracellular oxidation
state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen
peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally,
upon Cys oxidation PRDXs undergo extensive conformational rearrangements that
may underlie their presently structurally poorly defined functions as molecular
chaperones. Rearrangements include high molecular-weight oligomerization, the
dynamics of which are, however, poorly understood, as is the impact of disulfide
bond formation on these properties. Here we show that formation of disulfide bonds
along the catalytic cycle induces extensive μs time scale dynamics, as monitored
by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR
of a designed dimeric mutant. We ascribe the conformational dynamics to structural
frustration, resulting from conflicts between the disulfide-constrained reduction
of mobility and the desire to fulfill other favorable contacts.
acknowledgement: "We thank Albert A. Smith (Univ. Leipzig) for discussions and help
with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments
(Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis
script. Intramural funding from Institute of Science and Technology Austria is acknowledged.
This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG;
UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology
(PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both
platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges
funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish
Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through
a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre
for Molecular and Translational Medicine, University of Gothenburg, Sweden. "
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Troussicot, Laura
id: 3d9cac31-413c-11eb-9514-d1ec2a7fb7f3
last_name: Troussicot
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Mikael
full_name: Molin, Mikael
last_name: Molin
- first_name: Björn M.
full_name: Burmann, Björn M.
last_name: Burmann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal
of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200
apa: Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023).
Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin
from MAS NMR. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.3c01200
chicago: Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul
Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in
a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society.
American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.
ieee: L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,”
Journal of the American Chemical Society, vol. 145, no. 19. American Chemical
Society, pp. 10700–10711, 2023.
ista: Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal
of the American Chemical Society. 145(19), 10700–10711.
mla: Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and
Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American
Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711,
doi:10.1021/jacs.3c01200.
short: L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of
the American Chemical Society 145 (2023) 10700–10711.
date_created: 2023-05-28T22:01:04Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:48:09Z
day: '04'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1021/jacs.3c01200
external_id:
isi:
- '000985907400001'
pmid:
- '37140345'
file:
- access_level: open_access
checksum: 0758a930ef21c62fc91b14e657479f83
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:05:28Z
date_updated: 2023-05-30T07:05:28Z
file_id: '13098'
file_name: 2023_JACS_Troussicot.pdf
file_size: 6719299
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:05:28Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 10700–10711
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'
related_material:
record:
- id: '12820'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin
from MAS NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 145
year: '2023'
...
---
_id: '13042'
abstract:
- lang: eng
text: Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We
show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for
c>20, thus extending a result of Frieze and the author to smaller values of
c. Thereafter, for c>20, we determine the limit of the probability that
G(n, c/n)contains cycles of every length between the length of its shortest and its longest
cycles as n→∞.
acknowledgement: We would like to thank the reviewers for their helpful comments and
remarks.
article_number: P2.21
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: Anastos M. A note on long cycles in sparse random graphs. Electronic Journal
of Combinatorics. 2023;30(2). doi:10.37236/11471
apa: Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471
chicago: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471.
ieee: M. Anastos, “A note on long cycles in sparse random graphs,” Electronic
Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics,
2023.
ista: Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic
Journal of Combinatorics. 30(2), P2.21.
mla: Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic
Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics,
2023, doi:10.37236/11471.
short: M. Anastos, Electronic Journal of Combinatorics 30 (2023).
date_created: 2023-05-21T22:01:05Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-01T14:44:52Z
day: '05'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11471
external_id:
arxiv:
- '2105.13828'
isi:
- '000988285500001'
file:
- access_level: open_access
checksum: 6269ed3b3eded6536d3d9d6baad2d5b9
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:43:19Z
date_updated: 2023-05-22T07:43:19Z
file_id: '13046'
file_name: 2023_JourCombinatorics_Anastos.pdf
file_size: 448736
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:43:19Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on long cycles in sparse random graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2023'
...
---
_id: '12820'
abstract:
- lang: eng
text: "Disulfide bond formation is fundamentally important for protein structure,
and constitutes a key mechanism by which cells regulate the intracellular oxidation
state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen
peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally,
upon Cys oxidation PRDXs undergo extensive conformational rearrangements that
may underlie their presently structurally poorly defined functions as molecular
chaperones. Rearrangements include high molecular-weight oligomerization, the
dynamics of which are, however, poorly understood, as is the impact of disulfide
bond formation on these properties. Here we show that formation of disulfide bonds
along the catalytic cycle induces extensive microsecond time scale dynamics, as
monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly
and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics
to structural frustration, resulting from conflicts between the disulfide-constrained
reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis
data repository contains NMR data presented in the associated manuscript"
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Research data of the publication “Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820
apa: Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820
chicago: Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.
ieee: P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute
of Science and Technology Austria, 2023.
ista: Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.
mla: Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.
short: P. Schanda, (2023).
contributor:
- contributor_type: researcher
first_name: Laura
last_name: Troussicot
- contributor_type: researcher
first_name: Björn M.
last_name: Burmann
date_created: 2023-04-10T05:55:56Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:48:08Z
day: '18'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.15479/AT:ISTA:12820
file:
- access_level: open_access
checksum: 54a619605e44c871214fb0e07b05c6bf
content_type: application/zip
creator: pschanda
date_created: 2023-04-14T09:39:33Z
date_updated: 2023-04-14T09:39:33Z
file_id: '12823'
file_name: data_deposition.zip
file_size: 54184807
relation: main_file
success: 1
- access_level: open_access
checksum: 8dede9fc78399d13144eb05c62bf5750
content_type: application/octet-stream
creator: pschanda
date_created: 2023-04-14T09:39:58Z
date_updated: 2023-04-14T09:39:58Z
file_id: '12824'
file_name: README
file_size: 4978
relation: main_file
success: 1
file_date_updated: 2023-04-14T09:39:58Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13095'
relation: used_in_publication
status: public
status: public
title: Research data of the publication "Disulfide-bond-induced structural frustration
and dynamic disorder in a peroxiredoxin from MAS NMR"
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13092'
abstract:
- lang: eng
text: There is a need for the development of lead-free thermoelectric materials
for medium-/high-temperature applications. Here, we report a thiol-free tin telluride
(SnTe) precursor that can be thermally decomposed to produce SnTe crystals with
sizes ranging from tens to several hundreds of nanometers. We further engineer
SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing
the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles.
The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase
effectively improves the electrical conductivity of SnTe while simultaneously
reducing the lattice thermal conductivity without compromising the Seebeck coefficient.
Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit
up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared
with pristine SnTe.
acknowledgement: Open Access is funded by the Austrian Science Fund (FWF). We thank
Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X.,
and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support.
C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement
M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan
Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute
of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial
support from IST Austria.
article_processing_charge: No
article_type: original
author:
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Xuan
full_name: Song, Xuan
last_name: Song
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Linlin
full_name: Yang, Linlin
last_name: Yang
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric
composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389.
doi:10.1021/acsami.3c00625
apa: Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023).
Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials
and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625
chicago: Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona
Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS
Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625.
ieee: B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,”
ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical
Society, pp. 23380–23389, 2023.
ista: Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez
M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites.
ACS Applied Materials and Interfaces. 15(19), 23380–23389.
mla: Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.”
ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical
Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625.
short: B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H.
Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:50:09Z
day: '04'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsami.3c00625
external_id:
isi:
- '000985497900001'
pmid:
- '37141543'
file:
- access_level: open_access
checksum: 23893be46763c4c78daacddd019de821
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:38:44Z
date_updated: 2023-05-30T07:38:44Z
file_id: '13099'
file_name: 2023_ACSAppliedMaterials_Nan.pdf
file_size: 5640829
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:38:44Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 23380–23389
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bottom-up synthesis of SnTe-based thermoelectric composites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2023'
...
---
_id: '13094'
abstract:
- lang: eng
text: 'Endocytosis is a key cellular process involved in the uptake of nutrients,
pathogens, or the therapy of diseases. Most studies have focused on spherical
objects, whereas biologically relevant shapes can be highly anisotropic. In this
letter, we use an experimental model system based on Giant Unilamellar Vesicles
(GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first
stage of the passive endocytic process: engulfment of an anisotropic object by
the membrane. Our model has specific ligand–receptor interactions realized by
mobile receptors on the vesicles and immobile ligands on the particles. Through
a series of experiments, theory, and molecular dynamics simulations, we quantify
the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages
of the wrapping pathway. We find that the strong curvature variation in the neck
of the dumbbell as well as membrane tension are crucial in determining both the
speed of wrapping and the final states.'
acknowledgement: We sincerely thank Casper van der Wel for providing open-source packages
for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation
and Rachel Doherty for her assistance with particle functionalization. We are grateful
to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and
A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation
programme (ERC Starting Grant No. 802960).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ali
full_name: Azadbakht, Ali
last_name: Azadbakht
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
- first_name: Thijs
full_name: Varkevisser, Thijs
last_name: Varkevisser
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways
of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters.
2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375
apa: Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D.
J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar
Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375
chicago: Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and
Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant
Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.
ieee: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano
Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.
ista: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano
Letters. 23(10), 4267–4273.
mla: Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles
by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American
Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.
short: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano
Letters 23 (2023) 4267–4273.
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:51:25Z
day: '04'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1021/acs.nanolett.3c00375
ec_funded: 1
external_id:
isi:
- '000985481400001'
pmid:
- '37141427'
file:
- access_level: open_access
checksum: 9734d4c617bab3578ef62916b764547a
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:55:31Z
date_updated: 2023-05-30T07:55:31Z
file_id: '13100'
file_name: 2023_NanoLetters_Azadbakht.pdf
file_size: 3654910
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:55:31Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4267–4273
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2023'
...
---
_id: '13093'
abstract:
- lang: eng
text: The direct, solid state, and reversible conversion between heat and electricity
using thermoelectric devices finds numerous potential uses, especially around
room temperature. However, the relatively high material processing cost limits
their real applications. Silver selenide (Ag2Se) is one of the very few n-type
thermoelectric (TE) materials for room-temperature applications. Herein, we report
a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se,
which can be extended to other metal chalcogenides. These materials reach TE figures
of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide
(Bi2S3) particles also prepared in an aqueous solution are incorporated into the
Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt %
of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering.
The presence of Bi2S3 significantly improves the Seebeck coefficient and power
factor while at the same time decreasing the thermal conductivity with no apparent
drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved
in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT
value (zTave) of 0.93 in the 300–390 K range is demonstrated.
acknowledgement: 'Open Access is funded by the Austrian Science Fund (FWF). B.N.,
M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship
support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement
M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens
Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457
and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/.
ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.:
CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya.
J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and
projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges
support from the National Natural Science Foundation of China (22208293). This study
is part of the Advanced Materials programme and was supported by MCIN with funding
from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.'
article_processing_charge: No
article_type: original
author:
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Xu
full_name: Han, Xu
last_name: Han
- first_name: Yong
full_name: Zuo, Yong
last_name: Zuo
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based
on silver selenide in aqueous solution and ambient temperature. ACS Applied
Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055
apa: Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023).
Engineering of thermoelectric composites based on silver selenide in aqueous solution
and ambient temperature. ACS Applied Electronic Materials. American Chemical
Society. https://doi.org/10.1021/acsaelm.3c00055
chicago: Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang,
Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide
in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials.
American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055.
ieee: B. Nan et al., “Engineering of thermoelectric composites based on silver
selenide in aqueous solution and ambient temperature,” ACS Applied Electronic
Materials. American Chemical Society, 2023.
ista: Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol
J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites
based on silver selenide in aqueous solution and ambient temperature. ACS Applied
Electronic Materials.
mla: Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver
Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic
Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055.
short: B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J.
Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials
(2023).
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-01T14:50:48Z
day: '05'
department:
- _id: MaIb
doi: 10.1021/acsaelm.3c00055
external_id:
isi:
- '000986859000001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsaelm.3c00055
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: ACS Applied Electronic Materials
publication_identifier:
eissn:
- 2637-6113
publication_status: epub_ahead
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engineering of thermoelectric composites based on silver selenide in aqueous
solution and ambient temperature
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '13091'
abstract:
- lang: eng
text: We use a function field version of the Hardy–Littlewood circle method to study
the locus of free rational curves on an arbitrary smooth projective hypersurface
of sufficiently low degree. On the one hand this allows us to bound the dimension
of the singular locus of the moduli space of rational curves on such hypersurfaces
and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin
conjecture in terms of slopes with respect to the tangent bundle.
acknowledgement: The authors are grateful to Paul Nelson, Per Salberger and Jason
Starr for useful comments. While working on this paper the first author was supported
by EPRSC grant EP/P026710/1. The research was partially conducted during the period
the second author served as a Clay Research Fellow, and partially conducted during
the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and
the ETH Zurich Foundation.
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: Will
full_name: Sawin, Will
last_name: Sawin
citation:
ama: Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and
the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719
apa: Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree
hypersurfaces and the circle method. Algebra and Number Theory. Mathematical
Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719
chicago: Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree
Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical
Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719.
ieee: T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces
and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical
Sciences Publishers, pp. 719–748, 2023.
ista: Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces
and the circle method. Algebra and Number Theory. 17(3), 719–748.
mla: Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces
and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical
Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.
short: T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.
date_created: 2023-05-28T22:01:02Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2023-08-01T14:51:57Z
day: '12'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.2140/ant.2023.17.719
external_id:
arxiv:
- '1810.06882'
isi:
- '000996014700004'
file:
- access_level: open_access
checksum: 5d5d67b235905650e33cf7065d7583b4
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T08:05:22Z
date_updated: 2023-05-30T08:05:22Z
file_id: '13101'
file_name: 2023_AlgebraNumberTheory_Browning.pdf
file_size: 1430719
relation: main_file
success: 1
file_date_updated: 2023-05-30T08:05:22Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 719-748
project:
- _id: 26A8D266-B435-11E9-9278-68D0E5697425
grant_number: EP-P026710-2
name: Between rational and integral points
publication: Algebra and Number Theory
publication_identifier:
eissn:
- 1944-7833
issn:
- 1937-0652
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free rational curves on low degree hypersurfaces and the circle method
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2023'
...
---
_id: '13117'
abstract:
- lang: eng
text: The ability to control the direction of scattered light is crucial to provide
flexibility and scalability for a wide range of on-chip applications, such as
integrated photonics, quantum information processing, and nonlinear optics. Tunable
directionality can be achieved by applying external magnetic fields that modify
optical selection rules, by using nonlinear effects, or interactions with vibrations.
However, these approaches are less suitable to control microwave photon propagation
inside integrated superconducting quantum devices. Here, we demonstrate on-demand
tunable directional scattering based on two periodically modulated transmon qubits
coupled to a transmission line at a fixed distance. By changing the relative phase
between the modulation tones, we realize unidirectional forward or backward photon
scattering. Such an in-situ switchable mirror represents a versatile tool for
intra- and inter-chip microwave photonic processors. In the future, a lattice
of qubits can be used to realize topological circuits that exhibit strong nonreciprocity
or chirality.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski
for software development, and the MIBA workshop and the IST nanofabrication facility
for technical support. This work was supported by the Austrian Science Fund (FWF)
through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge
support from the European Research Council under grant agreement No 758053 (ERC
StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P.
has been supported by the Russian Science Foundation under the grant No 20-12-00194.
article_number: '2998'
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander V.
full_name: Poshakinskiy, Alexander V.
last_name: Poshakinskiy
- first_name: Riya
full_name: Sett, Riya
id: 2E6D040E-F248-11E8-B48F-1D18A9856A87
last_name: Sett
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Alexander N.
full_name: Poddubny, Alexander N.
last_name: Poddubny
- 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: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable
directional photon scattering from a pair of superconducting qubits. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38761-6
apa: Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N.,
& Fink, J. M. (2023). Tunable directional photon scattering from a pair of
superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6
chicago: Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka,
Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering
from a Pair of Superconducting Qubits.” Nature Communications. Springer
Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.
ieee: E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and
J. M. Fink, “Tunable directional photon scattering from a pair of superconducting
qubits,” Nature Communications, vol. 14. Springer Nature, 2023.
ista: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023.
Tunable directional photon scattering from a pair of superconducting qubits. Nature
Communications. 14, 2998.
mla: Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer
Nature, 2023, doi:10.1038/s41467-023-38761-6.
short: E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M.
Fink, Nature Communications 14 (2023).
date_created: 2023-06-04T22:01:02Z
date_published: 2023-05-24T00:00:00Z
date_updated: 2023-08-02T06:10:26Z
day: '24'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-023-38761-6
ec_funded: 1
external_id:
arxiv:
- '2205.03293'
isi:
- '001001099700002'
file:
- access_level: open_access
checksum: a857df40f0882859c48a1ff1e2001ec2
content_type: application/pdf
creator: dernst
date_created: 2023-06-06T07:31:20Z
date_updated: 2023-06-06T07:31:20Z
file_id: '13123'
file_name: 2023_NaturePhysics_Redchenko.pdf
file_size: 1654389
relation: main_file
success: 1
file_date_updated: 2023-06-06T07:31:20Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
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: 26B354CA-B435-11E9-9278-68D0E5697425
name: Controllable Collective States of Superconducting Qubit Ensembles
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13124'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Tunable directional photon scattering from a pair of superconducting qubits
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '13106'
abstract:
- lang: eng
text: Quantum entanglement is a key resource in currently developed quantum technologies.
Sharing this fragile property between superconducting microwave circuits and optical
or atomic systems would enable new functionalities, but this has been hindered
by an energy scale mismatch of >104 and the resulting mutually imposed loss and
noise. In this work, we created and verified entanglement between microwave and
optical fields in a millikelvin environment. Using an optically pulsed superconducting
electro-optical device, we show entanglement between propagating microwave and
optical fields in the continuous variable domain. This achievement not only paves
the way for entanglement between superconducting circuits and telecom wavelength
light, but also has wide-ranging implications for hybrid quantum networks in the
context of modularization, scaling, sensing, and cross-platform verification.
acknowledgement: This work was supported by the European Research Council (grant no.
758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation
Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support
from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship
with funding from the European Union’s Horizon 2020 Research and Innovation Program
(Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support
from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European
Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen
QUARTET).
article_processing_charge: No
article_type: original
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
- first_name: Y.
full_name: Minoguchi, Y.
last_name: Minoguchi
- first_name: P.
full_name: Rabl, P.
last_name: Rabl
- 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: Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science.
2023;380(6646):718-721. doi:10.1126/science.adg3812
apa: Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &
Fink, J. M. (2023). Entangling microwaves with light. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812
chicago: Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi,
P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science.
American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.
ieee: R. Sahu et al., “Entangling microwaves with light,” Science,
vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721,
2023.
ista: Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling
microwaves with light. Science. 380(6646), 718–721.
mla: Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol.
380, no. 6646, American Association for the Advancement of Science, 2023, pp.
718–21, doi:10.1126/science.adg3812.
short: R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink,
Science 380 (2023) 718–721.
date_created: 2023-05-31T11:39:24Z
date_published: 2023-05-18T00:00:00Z
date_updated: 2023-08-02T06:08:57Z
day: '18'
department:
- _id: JoFi
doi: 10.1126/science.adg3812
ec_funded: 1
external_id:
arxiv:
- '2301.03315'
isi:
- '000996515200004'
intvolume: ' 380'
isi: 1
issue: '6646'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.03315
month: '05'
oa: 1
oa_version: Preprint
page: 718-721
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: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/
record:
- id: '13122'
relation: research_data
status: public
status: public
title: Entangling microwaves with light
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 380
year: '2023'
...
---
_id: '13129'
abstract:
- lang: eng
text: "We study the representative volume element (RVE) method, which is a method
to approximately infer the effective behavior ahom of a stationary random medium.
The latter is described by a coefficient field a(x) generated from a given ensemble
⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory
of homogenization, the method proceeds by computing d=3 correctors (d denoting
the space dimension). To be numerically tractable, this computation has to be
done on a finite domain: the so-called representative volume element, i.e., a
large box with, say, periodic boundary conditions. The main message of this article
is: Periodize the ensemble instead of its realizations. By this, we mean that
it is better to sample from a suitably periodized ensemble than to periodically
extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩.
We make this point by investigating the bias (or systematic error), i.e., the
difference between ahom and the expected value of the RVE method, in terms of
its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x),
we heuristically argue that this error is generically O(L−1). In case of a suitable
periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give
a characterization of the leading-order error term for both strategies and argue
that even in the isotropic case it is generically non-degenerate. We carry out
the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian
type, which allow for a straightforward periodization, passing via the (integrable)
covariance function. This setting has also the advantage of making the Price theorem
and the Malliavin calculus available for optimal stochastic estimates of correctors.
We actually need control of second-order correctors to capture the leading-order
error term. This is due to inversion symmetry when applying the two-scale expansion
to the Green function. As a bonus, we present a stream-lined strategy to estimate
the error in a higher-order two-scale expansion of the Green function."
acknowledgement: 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: Nicolas
full_name: Clozeau, Nicolas
id: fea1b376-906f-11eb-847d-b2c0cf46455b
last_name: Clozeau
- first_name: Marc
full_name: Josien, Marc
last_name: Josien
- first_name: Felix
full_name: Otto, Felix
last_name: Otto
- first_name: Qiang
full_name: Xu, Qiang
last_name: Xu
citation:
ama: 'Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element
method: Periodize the ensemble instead of its realizations. Foundations of
Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y'
apa: 'Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative
volume element method: Periodize the ensemble instead of its realizations. Foundations
of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y'
chicago: 'Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the
Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.”
Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.'
ieee: 'N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume
element method: Periodize the ensemble instead of its realizations,” Foundations
of Computational Mathematics. Springer Nature, 2023.'
ista: 'Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume
element method: Periodize the ensemble instead of its realizations. Foundations
of Computational Mathematics.'
mla: 'Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method:
Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational
Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.'
short: N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics
(2023).
date_created: 2023-06-11T22:00:40Z
date_published: 2023-05-30T00:00:00Z
date_updated: 2023-08-02T06:12:39Z
day: '30'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s10208-023-09613-y
external_id:
isi:
- '000999623100001'
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10208-023-09613-y
month: '05'
oa: 1
oa_version: Published Version
publication: Foundations of Computational Mathematics
publication_identifier:
eissn:
- 1615-3383
issn:
- 1615-3375
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bias in the representative volume element method: Periodize the ensemble instead
of its realizations'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...