---
_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: '13039'
abstract:
- lang: eng
text: We calculate reflectivities of dynamically compressed water, water-ethanol
mixtures, and ammonia at infrared and optical wavelengths with density functional
theory and molecular dynamics simulations. The influence of the exchange-correlation
functional on the results is examined in detail. Our findings indicate that the
consistent use of the HSE hybrid functional reproduces experimental results much
better than the commonly used PBE functional. The HSE functional offers not only
a more accurate description of the electronic band gap but also shifts the onset
of molecular dissociation in the molecular dynamics simulations to significantly
higher pressures. We also highlight the importance of using accurate reference
standards in reflectivity experiments and reanalyze infrared and optical reflectivity
data from recent experiments. Thus, our combined theoretical and experimental
work explains and resolves lingering discrepancies between calculations and measurements
for the investigated molecular substances under shock compression.
acknowledgement: 'We thank R. Redmer for helpful discussions. M.F. acknowledges support
by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully
acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie
actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge
support form the French National Research Agency (ANR) through the projects POMPEI
(Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The
ab initio calculations were performed at the NorthGerman Supercomputing Alliance
(HLRN) facilities. '
article_number: '134109'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: French, Martin
last_name: French
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: Alessandra
full_name: Ravasio, Alessandra
last_name: Ravasio
- first_name: Jean Alexis
full_name: Hernandez, Jean Alexis
last_name: Hernandez
citation:
ama: French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of
the reflectivity of molecular fluids under shock compression. Physical Review
B. 2023;107(13). doi:10.1103/PhysRevB.107.134109
apa: French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab
initio calculation of the reflectivity of molecular fluids under shock compression.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109
chicago: French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis
Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under
Shock Compression.” Physical Review B. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevB.107.134109.
ieee: M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation
of the reflectivity of molecular fluids under shock compression,” Physical
Review B, vol. 107, no. 13. American Physical Society, 2023.
ista: French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation
of the reflectivity of molecular fluids under shock compression. Physical Review
B. 107(13), 134109.
mla: French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular
Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109,
American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109.
short: M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B
107 (2023).
date_created: 2023-05-21T22:01:04Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-01T14:45:25Z
day: '01'
department:
- _id: BiCh
doi: 10.1103/PhysRevB.107.134109
external_id:
isi:
- '000974672600001'
intvolume: ' 107'
isi: 1
issue: '13'
language:
- iso: eng
month: '04'
oa_version: None
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab initio calculation of the reflectivity of molecular fluids under shock compression
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
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'
...