---
_id: '12331'
abstract:
- lang: eng
text: High carrier mobility is critical to improving thermoelectric performance
over a broad temperature range. However, traditional doping inevitably deteriorates
carrier mobility. Herein, we develop a strategy for fine tuning of defects to
improve carrier mobility. To begin, n-type PbTe is created by compensating for
the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering,
resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is
introduced to compensate for the remaining intrinsic Pb vacancies. We find that
excess Ag exhibits a dynamic doping process with increasing temperatures, increasing
both the carrier concentration and carrier mobility throughout a wide temperature
range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained
for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier
concentration suppresses the bipolar thermal conductivity at high temperatures.
The final step is using iodine to optimize the carrier concentration to ∼1019
cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of
∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings
demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance
carrier mobility and improve thermoelectric performance.
acknowledgement: The National Key Research and Development Program of China (2018YFA0702100),
the Basic Science Center Project of the National Natural Science Foundation of China
(51788104), the National Natural Science Foundation of China (51571007 and 51772012),
the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the
National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise
Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Siqi
full_name: Wang, Siqi
last_name: Wang
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Shulin
full_name: Bai, Shulin
last_name: Bai
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Yingcai
full_name: Zhu, Yingcai
last_name: Zhu
- first_name: Shaoping
full_name: Zhan, Shaoping
last_name: Zhan
- first_name: Junqing
full_name: Zheng, Junqing
last_name: Zheng
- first_name: Shuwei
full_name: Tang, Shuwei
last_name: Tang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier
mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry
of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542
apa: Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023).
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. American Chemical Society.
https://doi.org/10.1021/acs.chemmater.2c03542
chicago: Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping
Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables
High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.”
Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.
ieee: S. Wang et al., “Fine tuning of defects enables high carrier mobility
and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials,
vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.
ista: Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023.
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.
mla: Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and
Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials,
vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.
short: S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D.
Zhao, Chemistry of Materials 35 (2023) 755–763.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-01-24T00:00:00Z
date_updated: 2023-08-14T12:57:44Z
day: '24'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acs.chemmater.2c03542
external_id:
isi:
- '000914749700001'
file:
- access_level: open_access
checksum: b21dca2aa7a80c068bc256bdd1fea9df
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T12:57:25Z
date_updated: 2023-08-14T12:57:25Z
file_id: '14055'
file_name: 2023_ChemistryMaterials_Wang.pdf
file_size: 2961043
relation: main_file
success: 1
file_date_updated: 2023-08-14T12:57:25Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 755-763
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Chemistry of Materials
publication_identifier:
eissn:
- 1520-5002
issn:
- 0897-4756
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '11999'
abstract:
- lang: eng
text: 'A simple drawing D(G) of a graph G is one where each pair of edges share
at most one point: either a common endpoint or a proper crossing. An edge e in
the complement of G can be inserted into D(G) if there exists a simple drawing
of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is
rectilinear (pseudolinear), that is, the edges can be extended into an arrangement
of lines (pseudolines), then any edge in the complement of G can be inserted.
In contrast, we show that it is NP-complete to decide whether one edge can be
inserted into a simple drawing. This remains true even if we assume that the drawing
is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles.
On the positive side, we show that, given an arrangement of pseudocircles A and
a pseudosegment σ, it can be decided in polynomial time whether there exists a
pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.'
acknowledgement: 'This work was started during the 6th Austrian–Japanese–Mexican–Spanish
Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants
for the good atmosphere as well as discussions on the topic. Also, we thank Jan
Kynčl for sending us remarks on a preliminary version of this work and an anonymous
referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie
grant agreement No 754411. Fabian Klute was partially supported by the Netherlands
Organisation for Scientific Research (NWO) under project no. 612.001.651 and by
the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were
partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative
DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was
also partially supported by the Independent Research Fund Denmark grant 2020-2023
(9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded
by the Ministry of Universities of Spain and the European Union (NextGenerationEU).
Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Fabian
full_name: Klute, Fabian
last_name: Klute
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
- first_name: Birgit
full_name: Vogtenhuber, Birgit
last_name: Vogtenhuber
- first_name: Raimund
full_name: Seidel, Raimund
last_name: Seidel
- first_name: Tilo
full_name: Wiedera, Tilo
last_name: Wiedera
citation:
ama: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting
one edge into a simple drawing is hard. Discrete and Computational Geometry.
2023;69:745–770. doi:10.1007/s00454-022-00394-9
apa: Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R.,
& Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9
chicago: Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber,
Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is
Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.
ieee: A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and
T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and
Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.
ista: Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T.
2023. Inserting one edge into a simple drawing is hard. Discrete and Computational
Geometry. 69, 745–770.
mla: Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is
Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023,
pp. 745–770, doi:10.1007/s00454-022-00394-9.
short: A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera,
Discrete and Computational Geometry 69 (2023) 745–770.
date_created: 2022-08-28T22:02:01Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-14T12:51:25Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/s00454-022-00394-9
ec_funded: 1
external_id:
arxiv:
- '1909.07347'
isi:
- '000840292800001'
file:
- access_level: open_access
checksum: def7ae3b28d9fd6aec16450e40090302
content_type: application/pdf
creator: alisjak
date_created: 2022-08-29T11:23:15Z
date_updated: 2022-08-29T11:23:15Z
file_id: '12006'
file_name: 2022_DiscreteandComputionalGeometry_Arroyo.pdf
file_size: 1002218
relation: main_file
success: 1
file_date_updated: 2022-08-29T11:23:15Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 745–770
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inserting one edge into a simple drawing is hard
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2023'
...
---
_id: '12330'
abstract:
- lang: eng
text: 'The design and implementation of efficient concurrent data structures has
seen significant attention. However, most of this work has focused on concurrent
data structures providing good worst-case guarantees, although, in real workloads,
objects are often accessed at different rates. Efficient distribution-adaptive
data structures, such as splay-trees, are known in the sequential case; however,
they often are hard to translate efficiently to the concurrent case. We investigate
distribution-adaptive concurrent data structures, and propose a new design called
the splay-list. At a high level, the splay-list is similar to a standard skip-list,
with the key distinction that the height of each element adapts dynamically to
its access rate: popular elements “move up,” whereas rarely-accessed elements
decrease in height. We show that the splay-list provides order-optimal amortized
complexity bounds for a subset of operations, while being amenable to efficient
concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity
for performance, and can outperform the only previously-known distribution-adaptive
concurrent design in certain workloads.'
article_processing_charge: No
article_type: original
author:
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Alexandra
full_name: Drozdova, Alexandra
last_name: Drozdova
- first_name: Amirkeivan
full_name: Mohtashami, Amirkeivan
last_name: Mohtashami
citation:
ama: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive
concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x'
apa: 'Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The
splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00441-x'
chicago: 'Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan
Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.'
ieee: 'V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list:
A distribution-adaptive concurrent skip-list,” Distributed Computing, vol.
36. Springer Nature, pp. 395–418, 2023.'
ista: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list:
A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.'
mla: 'Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent
Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp.
395–418, doi:10.1007/s00446-022-00441-x.'
short: V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing
36 (2023) 395–418.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-14T12:54:32Z
day: '01'
department:
- _id: DaAl
doi: 10.1007/s00446-022-00441-x
external_id:
arxiv:
- '2008.01009'
isi:
- '000913424000001'
intvolume: ' 36'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01009
month: '09'
oa: 1
oa_version: Preprint
page: 395-418
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The splay-list: A distribution-adaptive concurrent skip-list'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12114'
abstract:
- lang: eng
text: 'Probing the dynamics of aromatic side chains provides important insights
into the behavior of a protein because flips of aromatic rings in a protein’s
hydrophobic core report on breathing motion involving a large part of the protein.
Inherently invisible to crystallography, aromatic motions have been primarily
studied by solution NMR. The question how packing of proteins in crystals affects
ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning
NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a
protein in three different crystal packing environments to shed light onto possible
impact of packing on ring flips. The flips of the two Phe residues in ubiquitin,
both surface exposed, appear remarkably conserved in the different crystal forms,
even though the intermolecular packing is quite different: Phe4 flips on a ca.
10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to
µs motion. Our findings suggest that intramolecular influences are more important
for ring flips than intermolecular (packing) effects.'
acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within
the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche)
CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research
Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the
Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI
(ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership
for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing
and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg
State University in a form of the grant 92425251 and the access to the MRR, MCT
and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact
that “tensor asymmetry” is better called “tensor biaxiality”.
article_number: '100079'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Olga O.
full_name: Lebedenko, Olga O.
last_name: Lebedenko
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079'
apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R.,
Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079'
chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman
Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in
Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal
of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.'
ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin
protein crystals from MAS NMR and MD,” Journal of Structural Biology: X,
vol. 7. Elsevier, 2023.'
ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR,
Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals
from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.'
mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin
Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X,
vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.'
short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R.
Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).'
date_created: 2023-01-12T11:55:38Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-16T09:37:25Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.yjsbx.2022.100079
external_id:
pmid:
- '36578472'
file:
- access_level: open_access
checksum: b4b1c10a31018aafe053b7d55a470e54
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T09:36:28Z
date_updated: 2023-08-16T09:36:28Z
file_id: '14064'
file_name: 2023_JourStrucBiologyX_Gauto.pdf
file_size: 5132322
relation: main_file
success: 1
file_date_updated: 2023-08-16T09:36:28Z
has_accepted_license: '1'
intvolume: ' 7'
keyword:
- Structural Biology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Structural Biology: X'
publication_identifier:
issn:
- 2590-1524
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS
NMR and MD
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12163'
abstract:
- lang: eng
text: Small GTPases play essential roles in the organization of eukaryotic cells.
In recent years, it has become clear that their intracellular functions result
from intricate biochemical networks of the GTPase and their regulators that dynamically
bind to a membrane surface. Due to the inherent complexities of their interactions,
however, revealing the underlying mechanisms of action is often difficult to achieve
from in vivo studies. This review summarizes in vitro reconstitution approaches
developed to obtain a better mechanistic understanding of how small GTPase activities
are regulated in space and time.
acknowledgement: The authors acknowledge support from IST Austria and helpful comments
from the anonymous reviewers that helped to improve this manuscript. We apologize
to the authors of primary literature and outstanding research not cited here due
to space restraints.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: Hanifatul R
full_name: Budiman, Hanifatul R
id: 55380f95-15b2-11ec-abd3-aff8e230696b
last_name: Budiman
- first_name: Lukasz M
full_name: Kowalski, Lukasz M
id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2
last_name: Kowalski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
citation:
ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro
reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777.
doi:10.1002/1873-3468.14540
apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic,
I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters.
Wiley. https://doi.org/10.1002/1873-3468.14540
chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz
M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.
ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic,
“In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol.
597, no. 6. Wiley, pp. 762–777, 2023.
ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In
vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.
mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.
short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic,
FEBS Letters 597 (2023) 762–777.
date_created: 2023-01-12T12:09:58Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:32:29Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1002/1873-3468.14540
external_id:
isi:
- '000891573000001'
pmid:
- '36448231'
file:
- access_level: open_access
checksum: 7492244d3f9c5faa1347ef03f6e5bc84
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:31:04Z
date_updated: 2023-08-16T08:31:04Z
file_id: '14063'
file_name: 2023_FEBSLetters_Loose.pdf
file_size: 3148143
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:31:04Z
has_accepted_license: '1'
intvolume: ' 597'
isi: 1
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Biology
- Biochemistry
- Structural Biology
- Biophysics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 762-777
pmid: 1
publication: FEBS Letters
publication_identifier:
eissn:
- 1873-3468
issn:
- 0014-5793
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution of small GTPase regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 597
year: '2023'
...
---
_id: '12164'
abstract:
- lang: eng
text: 'A shared-memory counter is a widely-used and well-studied concurrent object.
It supports two operations: An Inc operation that increases its value by 1 and
a Read operation that returns its current value. In Jayanti et al (SIAM J Comput,
30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case
step complexity of obstruction-free implementations, from read-write registers,
of a large class of shared objects that includes counters. The lower bound leaves
open the question of finding counter implementations with sub-linear amortized
step complexity. In this work, we address this gap. We show that n-process, wait-free
and linearizable counters can be implemented from read-write registers with O(log2n)
amortized step complexity. This is the first counter algorithm from read-write
registers that provides sub-linear amortized step complexity in executions of
arbitrary length. Since a logarithmic lower bound on the amortized step complexity
of obstruction-free counter implementations exists, our upper bound is within
a logarithmic factor of the optimal. The worst-case step complexity of the construction
remains linear, which is optimal. This is obtained thanks to a new max register
construction with O(logn) amortized step complexity in executions of arbitrary
length in which the value stored in the register does not grow too quickly. We
then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel
[1] in which we “plug” our max register implementation to show that it remains
linearizable while achieving O(log2n) amortized step complexity.'
acknowledgement: A preliminary version of this work appeared in DISC’19. Mirza Ahad
Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes
and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported
by the Israel Science Foundation (Grants 380/18 and 1425/22).
article_processing_charge: No
article_type: original
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Danny
full_name: Hendler, Danny
last_name: Hendler
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5
apa: Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived
counters with polylogarithmic amortized step complexity. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00439-5
chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers.
“Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.
ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with
polylogarithmic amortized step complexity,” Distributed Computing, vol.
36. Springer Nature, pp. 29–43, 2023.
ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 36, 29–43.
mla: Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized
Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023,
pp. 29–43, doi:10.1007/s00446-022-00439-5.
short: M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023)
29–43.
date_created: 2023-01-12T12:10:08Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:39:36Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00446-022-00439-5
external_id:
isi:
- '000890138700001'
intvolume: ' 36'
isi: 1
keyword:
- Computational Theory and Mathematics
- Computer Networks and Communications
- Hardware and Architecture
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/
month: '03'
oa: 1
oa_version: Preprint
page: 29-43
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived counters with polylogarithmic amortized step complexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12515'
abstract:
- lang: eng
text: "Introduction: The olfactory system in most mammals is divided into several
subsystems based on the anatomical locations of the neuroreceptor cells involved
and the receptor families that are expressed. In addition to the main olfactory
system and the vomeronasal system, a range of olfactory subsystems converge onto
the transition zone located between the main olfactory bulb (MOB) and the accessory
olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL
contains specialized glomeruli that receive noncanonical sensory afferences and
which interact with the MOB and AOB. Little is known regarding the olfactory subsystems
of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing
the OL in the red fox by performing general and specific histological stainings
on serial sections, using both single and double immunohistochemical and lectin-histochemical
labeling techniques.\r\nResults: As a result, we have been able to determine that
the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development
and complexity.\r\nDiscussion: This makes this species a novel mammalian model,
the study of which could improve our understanding of the noncanonical pathways
involved in the processing of chemosensory cues."
acknowledgement: This work was partially supported by a grant from “Consello Social
Universidade de Santiago de Compostela” 2022-PU004.We would like to show special
gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing
us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia,
Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación
Galega de Caza for providing the red foxes used in this study.
article_number: '1097467'
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Ortiz-Leal, Irene
last_name: Ortiz-Leal
- first_name: Mateo V.
full_name: Torres, Mateo V.
last_name: Torres
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Luis Eusebio
full_name: Fidalgo, Luis Eusebio
last_name: Fidalgo
- first_name: Ana María
full_name: López-Beceiro, Ana María
last_name: López-Beceiro
- first_name: Jorge A.
full_name: Larriva-Sahd, Jorge A.
last_name: Larriva-Sahd
- first_name: Pablo
full_name: Sánchez-Quinteiro, Pablo
last_name: Sánchez-Quinteiro
citation:
ama: Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of
the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb
pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467
apa: Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro,
A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory
limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory
bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467
chicago: Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio
Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro.
“The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a
Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers,
2023. https://doi.org/10.3389/fnana.2022.1097467.
ieee: I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes
vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers
in Neuroanatomy, vol. 16. Frontiers, 2023.
ista: Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM,
Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox
(Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway.
Frontiers in Neuroanatomy. 16, 1097467.
mla: Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes).
New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in
Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.
short: I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro,
J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).
date_created: 2023-02-05T23:01:00Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-16T11:37:52Z
day: '10'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.3389/fnana.2022.1097467
external_id:
isi:
- '000919786900001'
pmid:
- '36704406'
file:
- access_level: open_access
checksum: 49cd40f3bda6f267079427042e7d15e3
content_type: application/pdf
creator: dernst
date_created: 2023-02-06T07:56:14Z
date_updated: 2023-02-06T07:56:14Z
file_id: '12518'
file_name: 2022_FrontiersNeuroanatomy_OrtizLeal.pdf
file_size: 21943473
relation: main_file
success: 1
file_date_updated: 2023-02-06T07:56:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neuroanatomy
publication_identifier:
eissn:
- 1662-5129
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding
a noncanonical olfactory bulb pathway
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-16T11:32:33Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
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- '000909067600003'
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language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2023'
...
---
_id: '12183'
abstract:
- lang: eng
text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with
Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii
regime, with an optimal bound on the condensate depletion. Moreover, our lower
bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann
bracketing) a lower bound for the ground state energy of N bosons in a large box
[−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions.
Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3
apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann
boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3
chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.
ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary
conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560,
2023.
ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary
conditions. Annales Henri Poincare. 24, 1505–1560.
mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.
short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.
date_created: 2023-01-15T23:00:52Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-16T11:34:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-022-01252-3
ec_funded: 1
external_id:
arxiv:
- '2205.15284'
isi:
- '000910751800002'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.15284
month: '05'
oa: 1
oa_version: Preprint
page: 1505-1560
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bose Gas in a box with Neumann boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12544'
abstract:
- lang: eng
text: Geometry is crucial in our efforts to comprehend the structures and dynamics
of biomolecules. For example, volume, surface area, and integrated mean and Gaussian
curvature of the union of balls representing a molecule are used to quantify its
interactions with the water surrounding it in the morphometric implicit solvent
models. The Alpha Shape theory provides an accurate and reliable method for computing
these geometric measures. In this paper, we derive homogeneous formulas for the
expressions of these measures and their derivatives with respect to the atomic
coordinates, and we provide algorithms that implement them into a new software
package, AlphaMol. The only variables in these formulas are the interatomic distances,
making them insensitive to translations and rotations. AlphaMol includes a sequential
algorithm and a parallel algorithm. In the parallel version, we partition the
atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree
algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented
by a buffer zone to account for atoms whose ball representations may partially
cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up
compared to an independent serial implementation when using 32 processors. For
instance, it takes 31 s to compute the geometric measures and derivatives of each
atom in a viral capsid with more than 26 million atoms on 32 Intel processors
running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant
computations, which ultimately limit the impact of using multiple processors.
AlphaMol is available as an OpenSource software.
acknowledgement: "P.K. acknowledges support from the University of California Multicampus
Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant
No.1760485). H.E. acknowledges support from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program, Grant No.
788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31,
and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access
is funded by the Austrian Science Fund (FWF)."
article_processing_charge: No
article_type: original
author:
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean,
and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346
apa: Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume,
surface area, mean, and Gaussian curvatures of molecules and their derivatives.
Journal of Chemical Information and Modeling. American Chemical Society.
https://doi.org/10.1021/acs.jcim.2c01346
chicago: Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the
Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.”
Journal of Chemical Information and Modeling. American Chemical Society,
2023. https://doi.org/10.1021/acs.jcim.2c01346.
ieee: P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface
area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal
of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society,
pp. 973–985, 2023.
ista: Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area,
mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 63(3), 973–985.
mla: Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian
Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information
and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85,
doi:10.1021/acs.jcim.2c01346.
short: P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and
Modeling 63 (2023) 973–985.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-02-13T00:00:00Z
date_updated: 2023-08-16T12:22:07Z
day: '13'
ddc:
- '510'
- '540'
department:
- _id: HeEd
doi: 10.1021/acs.jcim.2c01346
ec_funded: 1
external_id:
isi:
- '000920370700001'
pmid:
- '36638318'
file:
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content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:21:13Z
date_updated: 2023-08-16T12:21:13Z
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file_name: 2023_JCIM_Koehl.pdf
file_size: 8069223
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file_date_updated: 2023-08-16T12:21:13Z
has_accepted_license: '1'
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isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 973-985
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Journal of Chemical Information and Modeling
publication_identifier:
eissn:
- 1549-960X
issn:
- 1549-9596
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the volume, surface area, mean, and Gaussian curvatures of molecules
and their derivatives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2023'
...
---
_id: '12543'
abstract:
- lang: eng
text: Treating sick group members is a hallmark of collective disease defence in
vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness
and epidemiology, it is still largely unknown how pathogens react to the selection
pressure imposed by care intervention. Using social insects and pathogenic fungi,
we here performed a serial passage experiment in the presence or absence of colony
members, which provide social immunity by grooming off infectious spores from
exposed individuals. We found specific effects on pathogen diversity, virulence
and transmission. Under selection of social immunity, pathogens invested into
higher spore production, but spores were less virulent. Notably, they also elicited
a lower grooming response in colony members, compared with spores from the individual
host selection lines. Chemical spore analysis suggested that the spores from social
selection lines escaped the caregivers’ detection by containing lower levels of
ergosterol, a key fungal membrane component. Experimental application of chemically
pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated
cue triggering host social immunity against fungal pathogens. By reducing this
detection cue, pathogens were able to evade the otherwise very effective collective
disease defences of their social hosts.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the
fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team
at ISTA for ant collection and experimental help, in particular H. Leitner, and
the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg
and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the
Social Immunity team for comments on the manuscript. The study was funded by the
German Research Foundation (CR118/3-1) within the Framework of the Priority Program
SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon
2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Michaela
full_name: Hönigsberger, Michaela
id: 953894f3-25bd-11ec-8556-f70a9d38ef60
last_name: Hönigsberger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Niklas
full_name: Kampleitner, Niklas
id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87
last_name: Kampleitner
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6
apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F.,
Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature
Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6
chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse,
Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt,
and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and
Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.
ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology
and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.
ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner
N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 7, 450–460.
mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology
and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.
short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N.
Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution
7 (2023) 450–460.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T11:55:48Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
- _id: LifeSc
- _id: JiFr
doi: 10.1038/s41559-023-01981-6
ec_funded: 1
external_id:
isi:
- '000924572800001'
pmid:
- '36732670'
file:
- access_level: open_access
checksum: 8244f4650a0e7aeea488d1bcd4a31702
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:54:59Z
date_updated: 2023-08-16T11:54:59Z
file_id: '14069'
file_name: 2023_NatureEcoEvo_Stock.pdf
file_size: 1600499
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:54:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 450-460
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Nature Ecology and Evolution
publication_identifier:
eissn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/
scopus_import: '1'
status: public
title: Pathogen evasion of social immunity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-16T11:44:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
- '001021692200001'
pmid:
- '37065438'
file:
- access_level: open_access
checksum: a240a041cb9b9b7c8ba93a4706674a3f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:43:33Z
date_updated: 2023-08-16T11:43:33Z
file_id: '14068'
file_name: 2023_EvLetters_Mrnjavac.pdf
file_size: 2592189
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:43:33Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12679'
abstract:
- lang: eng
text: How to generate a brain of correct size and with appropriate cell-type diversity
during development is a major question in Neuroscience. In the developing neocortex,
radial glial progenitor (RGP) cells are the main neural stem cells that produce
cortical excitatory projection neurons, glial cells, and establish the prospective
postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated
developmental program that when disrupted can result in severe cortical malformations
such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms
instructing faithful RGP lineage progression are however not well understood.
This review will summarize recent conceptual advances that contribute to our understanding
of the general principles of RGP lineage progression.
acknowledgement: "I wish to thank all current and past members of the Hippenmeyer
laboratory at ISTA for exciting discussions on the subject of this review. I apologize
to colleagues whose work I could not cite and/or discuss in the frame of the available
space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported
by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council
(ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(grant agree-ment no. 725780 LinPro) to SH."
article_number: '102695'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Hippenmeyer S. Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4).
doi:10.1016/j.conb.2023.102695'
apa: 'Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology.
Elsevier. https://doi.org/10.1016/j.conb.2023.102695'
chicago: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression:
Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology.
Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.'
ieee: 'S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex,” Current Opinion in Neurobiology, vol.
79, no. 4. Elsevier, 2023.'
ista: 'Hippenmeyer S. 2023. Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4),
102695.'
mla: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights
from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol.
79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.'
short: S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).
date_created: 2023-02-26T12:24:21Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T12:30:25Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.conb.2023.102695
ec_funded: 1
external_id:
isi:
- '000953497700001'
pmid:
- '36842274'
file:
- access_level: open_access
checksum: 4d11c4ca87e6cbc4d2ac46d3225ea615
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:29:06Z
date_updated: 2023-08-16T12:29:06Z
file_id: '14071'
file_name: 2023_CurrentOpinionNeurobio_Hippenmeyer.pdf
file_size: 1787894
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:29:06Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '4'
keyword:
- General Neuroscience
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Principles of neural stem cell lineage progression: Insights from developing
cerebral cortex'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2023'
...
---
_id: '12429'
abstract:
- lang: eng
text: In this paper, we consider traces at initial times for functions with mixed
time-space smoothness. Such results are often needed in the theory of evolution
equations. Our result extends and unifies many previous results. Our main improvement
is that we can allow general interpolation couples. The abstract results are applied
to regularity problems for fractional evolution equations and stochastic evolution
equations, where uniform trace estimates on the half-line are shown.
acknowledgement: The first author has been partially supported by the Nachwuchsring—Network
for the promotion of young scientists—at TU Kaiserslautern. The second and third
authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation
for Scientific Research (NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Nick
full_name: Lindemulder, Nick
last_name: Lindemulder
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350.
doi:10.1002/mana.202100192
apa: Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding
and its applications to evolution equations. Mathematische Nachrichten.
Wiley. https://doi.org/10.1002/mana.202100192
chicago: Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding
and Its Applications to Evolution Equations.” Mathematische Nachrichten.
Wiley, 2023. https://doi.org/10.1002/mana.202100192.
ieee: A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its
applications to evolution equations,” Mathematische Nachrichten, vol. 296,
no. 4. Wiley, pp. 1319–1350, 2023.
ista: Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.
mla: Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution
Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp.
1319–50, doi:10.1002/mana.202100192.
short: A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023)
1319–1350.
date_created: 2023-01-29T23:00:59Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T11:41:42Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1002/mana.202100192
external_id:
arxiv:
- '2104.05063'
isi:
- '000914134900001'
file:
- access_level: open_access
checksum: 6f099f1d064173784d1a27716a2cc795
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:40:02Z
date_updated: 2023-08-16T11:40:02Z
file_id: '14067'
file_name: 2023_MathNachrichten_Agresti.pdf
file_size: 449280
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:40:02Z
has_accepted_license: '1'
intvolume: ' 296'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1319-1350
publication: Mathematische Nachrichten
publication_identifier:
eissn:
- 1522-2616
issn:
- 0025-584X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the trace embedding and its applications to evolution equations
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 296
year: '2023'
...
---
_id: '12430'
abstract:
- lang: eng
text: We study the time evolution of the Nelson model in a mean-field limit in which
N nonrelativistic bosons weakly couple (with respect to the particle number) to
a positive or zero mass quantized scalar field. Our main result is the derivation
of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove
the convergence of the approximate wave function to the many-body wave function
in norm, with a convergence rate proportional to the number of corrections taken
into account in the approximation. We prove an analogous result for the unitary
propagator. As an application, we derive a simple system of partial differential
equations describing the time evolution of the first- and second-order approximations
to the one-particle reduced density matrices of the particles and the quantum
field, respectively.
article_number: '2350006'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Falconi, Marco
last_name: Falconi
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order
corrections for the regularized Nelson model. Reviews in Mathematical Physics.
2023;35(4). doi:10.1142/S0129055X2350006X
apa: Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023).
Bogoliubov dynamics and higher-order corrections for the regularized Nelson model.
Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X
chicago: Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören
P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized
Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing,
2023. https://doi.org/10.1142/S0129055X2350006X.
ieee: M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov
dynamics and higher-order corrections for the regularized Nelson model,” Reviews
in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.
ista: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics
and higher-order corrections for the regularized Nelson model. Reviews in Mathematical
Physics. 35(4), 2350006.
mla: Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for
the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35,
no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.
short: M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical
Physics 35 (2023).
date_created: 2023-01-29T23:00:59Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-16T11:47:27Z
day: '09'
department:
- _id: RoSe
doi: 10.1142/S0129055X2350006X
external_id:
arxiv:
- '2110.00458'
isi:
- '000909760300001'
intvolume: ' 35'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2110.00458'
month: '01'
oa: 1
oa_version: Preprint
publication: Reviews in Mathematical Physics
publication_identifier:
issn:
- 0129-055X
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bogoliubov dynamics and higher-order corrections for the regularized Nelson
model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T12:41:53Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2023'
...
---
_id: '14085'
abstract:
- lang: eng
text: We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow
under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed,
unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm
in general sparse graphs with arbitrarily good approximation guarantee.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic
Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for
a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz
Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There,
he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich
Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster
and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their
insightful comments."
alternative_title:
- LIPIcs
article_number: '69'
article_processing_charge: Yes
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Goranci G, Henzinger MH. Efficient data structures for incremental exact and
approximate maximum flow. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.ICALP.2023.69'
apa: 'Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for
incremental exact and approximate maximum flow. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69'
chicago: Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for
Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.
ieee: G. Goranci and M. H. Henzinger, “Efficient data structures for incremental
exact and approximate maximum flow,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Goranci G, Henzinger MH. 2023. Efficient data structures for incremental
exact and approximate maximum flow. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 69.'
mla: Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata,
Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.
short: G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:00:49Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.69
ec_funded: 1
external_id:
unknown:
- '2211.09606'
file:
- access_level: open_access
checksum: 074177e815a1656de5d4071c7a3dffa6
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:59:05Z
date_updated: 2023-08-21T06:59:05Z
file_id: '14089'
file_name: 2023_LIPIcsICALP_Goranci.pdf
file_size: 875910
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:59:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient data structures for incremental exact and approximate maximum flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14084'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We will consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor
Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log
Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts
c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²)
samples for integer-valued distributions (ignoring some second-order terms and
parameters), We show this is optimal up to logarithmic factors. We illustrate
with improved algorithms for counting connected subgraphs and perfect matchings
in a graph."
acknowledgement: We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the
Wang-Landau algorithm and its use in physics.
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In:
50th International Colloquium on Automata, Languages, and Programming.
Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72'
apa: 'Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs
distributions. In 50th International Colloquium on Automata, Languages, and
Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72'
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” In 50th International Colloquium on Automata, Languages, and
Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
in 50th International Colloquium on Automata, Languages, and Programming,
Paderborn, Germany, 2023, vol. 261.
ista: 'Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions.
50th International Colloquium on Automata, Languages, and Programming. ICALP:
International Colloquium on Automata, Languages, and Programming, LIPIcs, vol.
261, 72.'
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.
short: D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T06:49:11Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: VlKo
doi: 10.4230/LIPIcs.ICALP.2023.72
external_id:
arxiv:
- '2007.10824'
file:
- access_level: open_access
checksum: 6dee0684245bb1c524b9c955db1e933d
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:45:16Z
date_updated: 2023-08-21T06:45:16Z
file_id: '14088'
file_name: 2023_LIPIcsICALP_Harris.pdf
file_size: 917791
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:45:16Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14086'
abstract:
- lang: eng
text: "The maximization of submodular functions have found widespread application
in areas such as machine learning, combinatorial optimization, and economics,
where practitioners often wish to enforce various constraints; the matroid constraint
has been investigated extensively due to its algorithmic properties and expressive
power. Though tight approximation algorithms for general matroid constraints exist
in theory, the running times of such algorithms typically scale quadratically,
and are not practical for truly large scale settings. Recent progress has focused
on fast algorithms for important classes of matroids given in explicit form. Currently,
nearly-linear time algorithms only exist for graphic and partition matroids [Alina
Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone
submodular maximization constrained by graphic, transversal matroids, or laminar
matroids in time near-linear in the size of their representation. Our algorithms
achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate
the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the
running time of our algorithm cannot be improved within the fast continuous greedy
framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák,
2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures
that maintain bases with approximate maximum cardinality and weight under certain
element updates. These data structures need to support a weight decrease operation
and a novel Freeze operation that allows the algorithm to freeze elements (i.e.
force to be contained) in its basis regardless of future data structure operations.
For the laminar matroid, we present a new dynamic data structure using the top
tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et
al., 2005] that maintains the maximum weight basis under insertions and deletions
of elements in O(log n) time. This data structure needs to support certain subtree
query and path update operations that are performed every insertion and deletion
that are non-trivial to handle in conjunction. For the transversal matroid the
Freeze operation corresponds to requiring the data structure to keep a certain
set S of vertices matched, a property that we call S-stability. While there is
a large body of work on dynamic matching algorithms, none are S-stable and maintain
an approximate maximum weight matching under vertex updates. We give the first
such algorithm for bipartite graphs with total running time linear (up to log
factors) in the number of edges."
acknowledgement: " Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast
Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by
NSF Award 2127781."
alternative_title:
- LIPIcs
article_number: '74'
article_processing_charge: Yes
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Paul
full_name: Liu, Paul
last_name: Liu
- first_name: Jan
full_name: Vondrák, Jan
last_name: Vondrák
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
citation:
ama: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for
several classes of matroids. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74'
apa: 'Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster
submodular maximization for several classes of matroids. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74'
chicago: Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular
Maximization for Several Classes of Matroids.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.
ieee: M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization
for several classes of matroids,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization
for several classes of matroids. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: International Colloquium on Automata, Languages, and Programming,
LIPIcs, vol. 261, 74.'
mla: Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes
of Matroids.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.
short: M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:05:47Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.74
ec_funded: 1
external_id:
arxiv:
- '2305.00122'
file:
- access_level: open_access
checksum: a5eef225014e003efbfbe4830fdd23cb
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:04:36Z
date_updated: 2023-08-21T07:04:36Z
file_id: '14090'
file_name: 2023_LIPIcsICALP_HenzingerM.pdf
file_size: 930943
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:04:36Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster submodular maximization for several classes of matroids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14083'
abstract:
- lang: eng
text: "In this work we consider the list-decodability and list-recoverability of
arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable
if every radius pn Hamming ball contains less than L codewords; (p,\U0001D4C1,L)_q-list-recoverability
is a generalization where we place radius pn Hamming balls on every point of a
combinatorial rectangle with side length \U0001D4C1 and again stipulate that there
be less than L codewords.\r\nOur main contribution is to precisely calculate the
maximum value of p for which there exist infinite families of positive rate (p,\U0001D4C1,L)_q-list-recoverable
codes, the quantity we call the zero-rate threshold. Denoting this value by p_*,
we in fact show that codes correcting a p_*+ε fraction of errors must have size
O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin
bound.\" To complement this, a standard random code with expurgation construction
shows that there exist positive rate codes correcting a p_*-ε fraction of errors.
We also follow a classical proof template (typically attributed to Elias and Bassalygo)
to derive from the zero-rate threshold other tradeoffs between rate and decoding
radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin
bound boils down to demonstrating the Schur convexity of a certain function defined
on the q-simplex as well as the convexity of a univariate function derived from
it. We remark that an earlier argument claimed similar results for q-ary list-decoding;
however, we point out that this earlier proof is flawed."
acknowledgement: "Nicolas Resch: Research supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research
and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the
National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements
YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions."
alternative_title:
- LIPIcs
article_number: '99'
article_processing_charge: Yes
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99'
apa: 'Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new
capacity bounds for list-decoding and list-recovery. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99'
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” In 50th International
Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 99.'
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” 50th International Colloquium on Automata, Languages, and
Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ICALP.2023.99.
short: N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:13Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:26:01Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.4230/LIPIcs.ICALP.2023.99
external_id:
arxiv:
- '2210.07754'
file:
- access_level: open_access
checksum: a449143fec3fbebb092cb8ef3b53c226
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:23:18Z
date_updated: 2023-08-21T07:23:18Z
file_id: '14091'
file_name: 2023_LIPIcsICALP_Resch.pdf
file_size: 1141497
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:23:18Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '12697'
abstract:
- lang: eng
text: Models for same-material contact electrification in granular media often rely
on a local charge-driving parameter whose spatial variations lead to a stochastic
origin for charge exchange. Measuring the charge transfer from individual granular
spheres after contacts with substrates of the same material, we find instead a
“global” charging behavior, coherent over the sample’s whole surface. Cleaning
and baking samples fully resets charging magnitude and direction, which indicates
the underlying global parameter is not intrinsic to the material, but acquired
from its history. Charging behavior is randomly and irreversibly affected by changes
in relative humidity, hinting at a mechanism where adsorbates, in particular,
water, are fundamental to the charge-transfer process.
acknowledgement: "We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti
for helpful discussions. This project has received funding from the European Research
Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant
Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation
program."
article_number: '098202'
article_processing_charge: No
article_type: original
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism
driven by sample history for contact electrification in granular media. Physical
Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202
apa: Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics
reveal a global mechanism driven by sample history for contact electrification
in granular media. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.130.098202
chicago: Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters. American Physical Society,
2023. https://doi.org/10.1103/physrevlett.130.098202.
ieee: G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal
a global mechanism driven by sample history for contact electrification in granular
media,” Physical Review Letters, vol. 130, no. 9. American Physical Society,
2023.
ista: Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global
mechanism driven by sample history for contact electrification in granular media.
Physical Review Letters. 130(9), 098202.
mla: Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics
Reveal a Global Mechanism Driven by Sample History for Contact Electrification
in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American
Physical Society, 2023, doi:10.1103/physrevlett.130.098202.
short: G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).
date_created: 2023-02-28T12:14:46Z
date_published: 2023-03-03T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '03'
ddc:
- '530'
- '537'
department:
- _id: ScWa
doi: 10.1103/physrevlett.130.098202
ec_funded: 1
external_id:
arxiv:
- '2211.02488'
isi:
- '000946178200008'
file:
- access_level: open_access
checksum: c4f2f6eea0408811f8f4898e15890355
content_type: application/pdf
creator: ggrosjea
date_created: 2023-02-28T12:20:27Z
date_updated: 2023-02-28T12:20:27Z
file_id: '12698'
file_name: Main_Preprint.pdf
file_size: 2301864
relation: main_file
success: 1
- access_level: open_access
checksum: 6af6ed6c97a977f923de4162294b43c4
content_type: application/pdf
creator: ggrosjea
date_created: 2023-02-28T12:20:55Z
date_updated: 2023-02-28T12:20:55Z
file_id: '12699'
file_name: Suppl_info.pdf
file_size: 1138625
relation: main_file
success: 1
- access_level: open_access
checksum: 3f20365fb9515bdba3a111d912c8d8b4
content_type: video/mp4
creator: ggrosjea
date_created: 2023-02-28T12:37:54Z
date_updated: 2023-02-28T12:37:54Z
file_id: '12700'
file_name: Suppl_vid1.mp4
file_size: 793449
relation: main_file
success: 1
- access_level: open_access
checksum: 90cecacbe0e2f9dea11f91a4ba20c32e
content_type: video/mp4
creator: ggrosjea
date_created: 2023-02-28T12:37:54Z
date_updated: 2023-02-28T12:37:54Z
file_id: '12701'
file_name: Suppl_vid2.mp4
file_size: 455925
relation: main_file
success: 1
file_date_updated: 2023-02-28T12:37:54Z
has_accepted_license: '1'
intvolume: ' 130'
isi: 1
issue: '9'
keyword:
- General Physics
- Electrostatics
- Triboelectricity
- Soft Matter
- Acoustic Levitation
- Granular Materials
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2211.02488
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '8101'
relation: research_paper
status: public
status: public
title: Single-collision statistics reveal a global mechanism driven by sample history
for contact electrification in granular media
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: 130
year: '2023'
...
---
_id: '13175'
abstract:
- lang: eng
text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13175
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:13175.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-06-30T08:07:43Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-24T11:16:35Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:13175
ec_funded: 1
file:
- access_level: open_access
checksum: 7d03f1a5a5258ee43dfc3323dea4e08f
content_type: application/pdf
creator: cchlebak
date_created: 2023-06-30T08:17:25Z
date_updated: 2023-06-30T08:17:25Z
file_id: '13176'
file_name: thesis_pdfa.pdf
file_size: 18688376
relation: main_file
success: 1
- access_level: closed
checksum: c3b45317ae58e0527533f98c202d81b7
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-07-06T11:35:15Z
date_updated: 2023-07-06T11:35:15Z
file_id: '13196'
file_name: thesis.zip
file_size: 37847025
relation: source_file
file_date_updated: 2023-07-06T11:35:15Z
has_accepted_license: '1'
keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '202'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12900'
relation: old_edition
status: public
- id: '10924'
relation: part_of_dissertation
status: public
- id: '9114'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14242'
abstract:
- lang: eng
text: We study the problem of training and certifying adversarially robust quantized
neural networks (QNNs). Quantization is a technique for making neural networks
more efficient by running them using low-bit integer arithmetic and is therefore
commonly adopted in industry. Recent work has shown that floating-point neural
networks that have been verified to be robust can become vulnerable to adversarial
attacks after quantization, and certification of the quantized representation
is necessary to guarantee robustness. In this work, we present quantization-aware
interval bound propagation (QA-IBP), a novel method for training robust QNNs.
Inspired by advances in robust learning of non-quantized networks, our training
algorithm computes the gradient of an abstract representation of the actual network.
Unlike existing approaches, our method can handle the discrete semantics of QNNs.
Based on QA-IBP, we also develop a complete verification procedure for verifying
the adversarial robustness of QNNs, which is guaranteed to terminate and produce
a correct answer. Compared to existing approaches, the key advantage of our verification
procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate
experimentally that our approach significantly outperforms existing methods and
establish the new state-of-the-art for training and certifying the robustness
of QNNs.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research
was sponsored by the United\r\nStates Air Force Research Laboratory and the United
States Air Force Artificial Intelligence Accelerator and was accomplished under
Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained
in this document are those of the authors and should not be interpreted as representing
the official policies, either expressed or implied,\r\nof the United States Air
Force or the U.S. Government. The U.S. Government is authorized to reproduce and
distribute reprints for Government purposes notwithstanding any copyright\r\nnotation
herein. The research was also funded in part by the AI2050 program at Schmidt Futures
(Grant G-22-63172) and Capgemini SE."
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973.
doi:10.1609/aaai.v37i12.26747'
apa: 'Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D.
(2023). Quantization-aware interval bound propagation for training certifiably
robust quantized neural networks. In Proceedings of the 37th AAAI Conference
on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747'
chicago: Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger,
and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably
Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 37:14964–73. Association for the Advancement of
Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.
ieee: M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks,”
in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.
ista: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference
on Artificial Intelligence vol. 37, 14964–14973.'
mla: Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for
Training Certifiably Robust Quantized Neural Networks.” Proceedings of the
37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association
for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.
short: M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 14964–14973.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:17Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2023-09-05T07:06:14Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i12.26747
ec_funded: 1
external_id:
arxiv:
- '2211.16187'
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.16187
month: '06'
oa: 1
oa_version: Preprint
page: 14964-14973
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantization-aware interval bound propagation for training certifiably robust
quantized neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14243'
abstract:
- lang: eng
text: 'Two-player zero-sum "graph games" are central in logic, verification, and
multi-agent systems. The game proceeds by placing a token on a vertex of a graph,
and allowing the players to move it to produce an infinite path, which determines
the winner or payoff of the game. Traditionally, the players alternate turns in
moving the token. In "bidding games", however, the players have budgets and in
each turn, an auction (bidding) determines which player moves the token. So far,
bidding games have only been studied as full-information games. In this work we
initiate the study of partial-information bidding games: we study bidding games
in which a player''s initial budget is drawn from a known probability distribution.
We show that while for some bidding mechanisms and objectives, it is straightforward
to adapt the results from the full-information setting to the partial-information
setting, for others, the analysis is significantly more challenging, requires
new techniques, and gives rise to interesting results. Specifically, we study
games with "mean-payoff" objectives in combination with "poorman" bidding. We
construct optimal strategies for a partially-informed player who plays against
a fully-informed adversary. We show that, somewhat surprisingly, the "value" under
pure strategies does not necessarily exist in such games.'
acknowledgement: This research was supported in part by ISF grant no.1679/21, by the
ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable
budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679'
apa: Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with
partially-observable budgets. In Proceedings of the 37th AAAI Conference on
Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States.
https://doi.org/10.1609/aaai.v37i5.25679
chicago: Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with
Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on
Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.
ieee: G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable
budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.
ista: 'Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable
budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI:
Conference on Artificial Intelligence vol. 37, 5464–5471.'
mla: Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.”
Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol.
37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.
short: G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 2023, pp. 5464–5471.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:18Z
date_published: 2023-06-27T00:00:00Z
date_updated: 2023-09-05T08:37:00Z
day: '27'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i5.25679
ec_funded: 1
external_id:
arxiv:
- '2211.13626'
intvolume: ' 37'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1609/aaai.v37i5.25679
month: '06'
oa: 1
oa_version: Published Version
page: 5464-5471
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bidding graph games with partially-observable budgets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14241'
abstract:
- lang: eng
text: We present a technique to optimize the reflectivity of a surface while preserving
its overall shape. The naïve optimization of the mesh vertices using the gradients
of reflectivity simulations results in undesirable distortion. In contrast, our
robust formulation optimizes the surface normal as an independent variable that
bridges the reflectivity term with differential rendering, and the regularization
term with as-rigid-as-possible elastic energy. We further adaptively subdivide
the input mesh to improve the convergence. Consequently, our method can minimize
the retroreflectivity of a wide range of input shapes, resulting in sharply creased
shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by
changing the reward for the direction of the outgoing light directions, our method
can be applied to other reflectivity design tasks, such as the optimization of
architectural walls to concentrate light in a specific region. We have tested
the proposed method using light-transport simulations and real-world 3D-printed
objects.
acknowledgement: "The authors would like to thank Yuki Koyama and Takeo Igarashi for
early discussions, and Yuta Yaguchi for support in 3D printing. This research is
partially supported by the Israel Science Foundation grant number 1390/19.\r\n"
article_number: '20'
article_processing_charge: No
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization
as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association
for Computing Machinery; 2023. doi:10.1145/3588432.3591542'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper:
Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference
Proceedings. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3588432.3591542'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth
Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023
Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity
optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings,
Los Angeles, CA, United States, 2023.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity
optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH:
Computer Graphics and Interactive Techniques Conference, 20.'
mla: 'Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface
Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for
Computing Machinery, 2023, doi:10.1145/3588432.3591542.'
short: K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference
Proceedings, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
date_created: 2023-08-27T22:01:17Z
date_published: 2023-07-23T00:00:00Z
date_updated: 2023-09-05T07:22:03Z
day: '23'
department:
- _id: BeBi
doi: 10.1145/3588432.3591542
external_id:
arxiv:
- '2305.05944'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.05944
month: '07'
oa: 1
oa_version: Preprint
publication: SIGGRAPH 2023 Conference Proceedings
publication_identifier:
isbn:
- '9798400701597'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Stealth shaper: Reflectivity optimization as surface stylization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13310'
abstract:
- lang: eng
text: Machine-learned systems are in widespread use for making decisions about humans,
and it is important that they are fair, i.e., not biased against individuals based
on sensitive attributes. We present runtime verification of algorithmic fairness
for systems whose models are unknown, but are assumed to have a Markov chain structure.
We introduce a specification language that can model many common algorithmic fairness
properties, such as demographic parity, equal opportunity, and social burden.
We build monitors that observe a long sequence of events as generated by a given
system, and output, after each observation, a quantitative estimate of how fair
or biased the system was on that run until that point in time. The estimate is
proven to be correct modulo a variable error bound and a given confidence level,
where the error bound gets tighter as the observed sequence gets longer. Our monitors
are of two types, and use, respectively, frequentist and Bayesian statistical
inference techniques. While the frequentist monitors compute estimates that are
objectively correct with respect to the ground truth, the Bayesian monitors compute
estimates that are correct subject to a given prior belief about the system’s
model. Using a prototype implementation, we show how we can monitor if a bank
is fair in giving loans to applicants from different social backgrounds, and if
a college is fair in admitting students while maintaining a reasonable financial
burden on the society. Although they exhibit different theoretical complexities
in certain cases, in our experiments, both frequentist and Bayesian monitors took
less than a millisecond to update their verdicts after each observation.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG101020093.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mahyar
full_name: Karimi, Mahyar
id: f1dedef5-2f78-11ee-989a-c4c97bccf506
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness.
In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382.
doi:10.1007/978-3-031-37703-7_17'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring
algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382).
Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17'
chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.
ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic
fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965,
pp. 358–382.
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic
fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13965, 358–382.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer
Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.
short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 358–382.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-07-25T18:32:40Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-05T15:14:00Z
day: '18'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-37703-7_17
ec_funded: 1
external_id:
arxiv:
- '2305.15979'
file:
- access_level: open_access
checksum: ccaf94bf7d658ba012c016e11869b54c
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:11:20Z
date_updated: 2023-07-31T08:11:20Z
file_id: '13327'
file_name: 2023_LNCS_CAV_HenzingerT.pdf
file_size: 647760
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:11:20Z
has_accepted_license: '1'
intvolume: ' 13965'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 358–382
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377037'
eissn:
- 1611-3349
isbn:
- '9783031377020'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Monitoring algorithmic fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13965
year: '2023'
...
---
_id: '12205'
abstract:
- lang: eng
text: "Background: This study seeks to evaluate the impact of breast cancer (BRCA)
gene status on tumor dissemination pattern, surgical outcome and survival in a
multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian
cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data
from 190 patients were gathered retrospectively. All patients had surgery at pOC
and at least one further rOC surgery at four European high-volume centers. Patients
were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut)
and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor
presentation, surgical outcome and survival data were analyzed between the two
groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years
younger and had significantly more tumor involvement upon diagnosis. Patients
with BRCAmut disease showed higher debulking rates at all stages. Multivariate
analysis showed that only patient age had significant predictive value for complete
tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated
with optimal debulking. Patients with BRCAmut disease showed significantly prolonged
overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged
in the BRCAmut group at all stages as well, reaching statistical significance
during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a
more aggressive course of disease with earlier onset and more extensive tumor
dissemination at pOC. However, surgical outcome and OS were significantly better
in patients with BRCAmut disease compared with patients with BRCAwt disease. We
therefore propose to consider BRCAmut status in regard to patient selection for
cytoreductive surgery, especially in rOC."
acknowledgement: "E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a
participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin
Berlin and the Berlin Institute of Health. This work was supported by European Commission’s
Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen
Access funding enabled and organized by Projekt DEAL."
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome and patient survival in primary
and recurrent high-grade serous ovarian cancer: A multicenter retrospective study
by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium.
Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical
Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation
Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in
Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective
Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.”
Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.'
ieee: 'J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of
Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.'
mla: 'Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination
Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade
Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of
Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 35–45.
date_created: 2023-01-16T09:44:36Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:37Z
day: '01'
ddc:
- '610'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12459-3
external_id:
isi:
- '000852125500006'
file:
- access_level: open_access
checksum: 36a1200e1011f4b2155a8041d0308f34
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T13:01:20Z
date_updated: 2023-02-02T13:01:20Z
file_id: '12490'
file_name: 2023_AnnalsSurgicalOncology_Glajzer.pdf
file_size: 365865
relation: main_file
success: 1
file_date_updated: 2023-02-02T13:01:20Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 35-45
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12115'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '12115'
acknowledgement: This work was supported by European Commission’s Seventh Framework
Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact
of BRCA mutation status on tumor dissemination pattern, surgical outcome, and
patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC).
A multicenter, retrospective study of the ovarian cancer therapy—innovative models
prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47.
doi:10.1245/s10434-022-12681-z'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract:
Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome,
and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer
(HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative
Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology.
Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.'
ieee: 'J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp.
46–47, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern,
surgical outcome, and patient survival in primary and recurrent high-grade serous
ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer
therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical
Oncology. 30, 46–47.'
mla: 'Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status
on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary
and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective
Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS)
Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023,
pp. 46–47, doi:10.1245/s10434-022-12681-z.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 46–47.
date_created: 2023-01-12T11:56:22Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:36Z
day: '01'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12681-z
external_id:
isi:
- '000879151800001'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1245/s10434-022-12681-z
month: '01'
oa: 1
oa_version: Published Version
page: 46-47
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12205'
relation: other
status: public
scopus_import: '1'
status: public
title: 'ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome, and patient survival in primary and recurrent high-grade
serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian
cancer therapy—innovative models prolong survival (OCTIPS) consortium'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '14253'
abstract:
- lang: eng
text: Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM)
are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration
of intracellular signaling machinery near ER-PM junctions allows these domains
to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular
compartmentalization of protein kinase A (PKA) signaling also regulates essential
cellular functions, however, no specific association between PKA and ER-PM junctional
domains is known. Here, we show that in brain neurons type I PKA is directed to
Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific
anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and
ER-resident VAP proteins results in the concentration of type I PKA between stacked
ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome
enables reciprocal regulation between PKA and Ca2+ signaling machinery to support
Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal
ER-PM junctions support a receptor-independent form of PKA signaling driven by
membrane depolarization and intracellular Ca2+, allowing conversion of information
encoded in electrical signals into biochemical changes universally recognized
throughout the cell.
acknowledgement: We thank Kayla Templeton and Peter Turcanu for technical assistance,
Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin
Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn
Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for
assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful
discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also
thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used
in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648
(J.S.T.), and F32NS108519 (N.C.V.).
article_number: '5231'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicholas C.
full_name: Vierra, Nicholas C.
last_name: Vierra
- first_name: Luisa
full_name: Ribeiro-Silva, Luisa
last_name: Ribeiro-Silva
- first_name: Michael
full_name: Kirmiz, Michael
last_name: Kirmiz
- first_name: Deborah
full_name: Van Der List, Deborah
last_name: Van Der List
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Olivia A.
full_name: Mack, Olivia A.
last_name: Mack
- first_name: James
full_name: Carroll, James
last_name: Carroll
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Sue A.
full_name: Aicher, Sue A.
last_name: Aicher
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: James S.
full_name: Trimmer, James S.
last_name: Trimmer
citation:
ama: Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions
couple excitation to Ca2+-activated PKA signaling. Nature Communications.
2023;14. doi:10.1038/s41467-023-40930-6
apa: Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P.,
Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-40930-6
chicago: Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der
List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma
Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.
ieee: N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling,” Nature Communications, vol.
14. Springer Nature, 2023.
ista: Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA,
Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma
membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications.
14, 5231.
mla: Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation
to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231,
Springer Nature, 2023, doi:10.1038/s41467-023-40930-6.
short: N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A.
Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature
Communications 14 (2023).
date_created: 2023-09-03T22:01:14Z
date_published: 2023-08-26T00:00:00Z
date_updated: 2023-09-06T06:53:32Z
day: '26'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1038/s41467-023-40930-6
external_id:
pmid:
- '37633939'
file:
- access_level: open_access
checksum: 6ab8aab4e957f626a09a1c73db3388fb
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T06:50:07Z
date_updated: 2023-09-06T06:50:07Z
file_id: '14270'
file_name: 2023_NatureComm_Vierra.pdf
file_size: 9412549
relation: main_file
success: 1
file_date_updated: 2023-09-06T06:50:07Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '08'
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: Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA
signaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14259'
abstract:
- lang: eng
text: "We provide a learning-based technique for guessing a winning strategy in
a parity game originating from an LTL synthesis problem. A cheaply obtained guess
can be useful in several applications. Not only can the guessed strategy be applied
as best-effort in cases where the game’s huge size prohibits rigorous approaches,
but it can also increase the scalability of rigorous LTL synthesis in several
ways. Firstly, checking whether a guessed strategy is winning is easier than constructing
one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy
iteration faster than constructing one from scratch. Thirdly, the guess can be
used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn
contrast to previous works, we (i) reflect the highly structured logical information
in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata
translations, and (ii) learn to reflect it properly by learning from previously
solved games, bringing the solving process closer to human-like reasoning."
acknowledgement: This research was funded in part by the German Research Foundation
(DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Maximilian
full_name: Prokop, Maximilian
last_name: Prokop
- first_name: Sabine
full_name: Rieder, Sabine
last_name: Rieder
citation:
ama: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies
in LTL synthesis by semantic learning. In: 35th International Conference on
Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20'
apa: 'Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing
winning policies in LTL synthesis by semantic learning. In 35th International
Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris,
France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder.
“Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th
International Conference on Computer Aided Verification , 13964:390–414. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.
ieee: J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning
policies in LTL synthesis by semantic learning,” in 35th International Conference
on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.
ista: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies
in LTL synthesis by semantic learning. 35th International Conference on Computer
Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.'
mla: Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic
Learning.” 35th International Conference on Computer Aided Verification ,
vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.
short: J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International
Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-06T08:27:33Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37706-8_20
file:
- access_level: open_access
checksum: ed66278b61bb869e1baba3d9b9081271
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:25:50Z
date_updated: 2023-09-06T08:25:50Z
file_id: '14276'
file_name: 2023_LNCS_CAV_Kretinsky.pdf
file_size: 428354
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:25:50Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 390-414
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guessing winning policies in LTL synthesis by semantic learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14256'
abstract:
- lang: eng
text: "Context. Space asteroseismology is revolutionizing our knowledge of the internal
structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries
of signatures of strong magnetic fields in the core of red giant stars. The key
signature for such a detection is the asymmetry these fields induce in the frequency
splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate
the ability of the observed asymmetries of the frequency splittings of dipolar
mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods.
We used the powerful analytical Racah-Wigner algebra used in quantum mechanics
to characterize the geometrical couplings of dipolar mixed oscillation modes with
various realistically plausible topologies of fossil magnetic fields. We also
computed the induced perturbation of their frequencies.\r\nResults. First, in
the case of an oblique magnetic dipole, we provide the exact analytical expression
of the asymmetry as a function of the angle between the rotation and magnetic
axes. Its value provides a direct measure of this angle. Second, considering a
combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry
is blind to the unraveling of the relative strength and sign of each component.
Finally, in the case of a given multipole, we show that a negative asymmetry is
a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar
mixed modes provide a key bit of information on the geometrical topology of deep
fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints
should therefore be combined with spectropolarimetric observations and numerical
simulations, which aim to predict the more probable stable large-scale geometries."
acknowledgement: The authors are grateful to the referee for her/his detailed and
constructive report, which has allowed us to improve our article. S. M. acknowledges
support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU).
We thank R. A. Garcia for fruitful discussions and suggestions.
article_number: L9
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
author:
- first_name: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: 'Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed
modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
2023;676. doi:10.1051/0004-6361/202346832'
apa: 'Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings
of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy
and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832'
chicago: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.'
ieee: 'S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields,” Astronomy and
Astrophysics, vol. 676. EDP Sciences, 2023.'
ista: 'Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
676, L9.'
mla: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.'
short: S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-09-06T11:05:58Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202346832
external_id:
arxiv:
- '2306.11587'
isi:
- '001046037700007'
file:
- access_level: open_access
checksum: 7b30d26fb2b7bcb5b5be1414950615f9
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:13:19Z
date_updated: 2023-09-06T07:13:19Z
file_id: '14271'
file_name: 2023_AstronomyAstrophysics_Mathis.pdf
file_size: 458120
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:13:19Z
has_accepted_license: '1'
intvolume: ' 676'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Asymmetries of frequency splittings of dipolar mixed modes: A window on the
topology of deep magnetic fields'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 676
year: '2023'
...
---
_id: '14261'
abstract:
- lang: eng
text: In this work, a generalized, adapted Numerov implementation capable of determining
band structures of periodic quantum systems is outlined. Based on the input potential,
the presented approach numerically solves the Schrödinger equation in position
space at each momentum space point. Thus, in addition to the band structure, the
method inherently provides information about the state functions and probability
densities in position space at each momentum space point considered. The generalized,
adapted Numerov framework provided reliable estimates for a variety of increasingly
complex test suites in one, two, and three dimensions. The accuracy of the proposed
methodology was benchmarked against results obtained for the analytically solvable
Kronig-Penney model. Furthermore, the presented numerical solver was applied to
a model potential representing a 2D optical lattice being a challenging application
relevant, for example, in the field of quantum computing.
acknowledgement: Financial supports for this work via a PhD scholarship for J. Gamper
issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike
Tanzer) are gratefully acknowledged. The computational results presented have been
achieved (in part) using the HPC infrastructure of the University of Innsbruck.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jakob
full_name: Gamper, Jakob
last_name: Gamper
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Alexander K.H.
full_name: Weiss, Alexander K.H.
last_name: Weiss
- first_name: Thomas S.
full_name: Hofer, Thomas S.
last_name: Hofer
citation:
ama: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave
functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707
apa: Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023).
Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems. Journal of Physical Chemistry Letters. American Chemical
Society. https://doi.org/10.1021/acs.jpclett.3c01707
chicago: Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas
S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations
of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-,
Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry
Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.
ieee: J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position
space wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems,”
Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical
Society, pp. 7395–7403, 2023.
ista: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space
wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 14(33), 7395–7403.
mla: Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure
Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation
for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical
Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403,
doi:10.1021/acs.jpclett.3c01707.
short: J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical
Chemistry Letters 14 (2023) 7395–7403.
date_created: 2023-09-03T22:01:16Z
date_published: 2023-08-11T00:00:00Z
date_updated: 2023-09-06T11:04:31Z
day: '11'
ddc:
- '530'
- '540'
department:
- _id: GradSch
doi: 10.1021/acs.jpclett.3c01707
external_id:
isi:
- '001048165800001'
pmid:
- '37566743'
file:
- access_level: open_access
checksum: 637454e2b3a357498d8d622d241c4bf6
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:32:39Z
date_updated: 2023-09-06T07:32:39Z
file_id: '14272'
file_name: 2023_JourPhysChemistry_Gamper.pdf
file_size: 4986859
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:32:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 7395-7403
pmid: 1
publication: Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2023'
...
---
_id: '14277'
abstract:
- lang: eng
text: Living tissues are characterized by an intrinsically mechanochemical interplay
of active physical forces and complex biochemical signaling pathways. Either feature
alone can give rise to complex emergent phenomena, for example, mechanically driven
glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion
instabilities. An important question is how to quantitatively assess the contribution
of these different cues to the large-scale dynamics of biological materials. We
address this in Madin-Darby canine kidney (MDCK) monolayers, considering both
mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling
activity and cellular density as well as a mechanically active tissue rheology
via a self-propelled vertex model. We show that the relative strength of active
migration forces to mechanochemical couplings controls a transition from a uniform
active glass to periodic spatiotemporal waves. We parametrize the model from published
experimental data sets on MDCK monolayers and use it to make new predictions on
the correlation functions of cellular dynamics and the dynamics of topological
defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers
are best described by an intermediary parameter region in which both mechanochemical
couplings and noisy active propulsion have a strong influence on the dynamics.
Finally, we study how tissue rheology and ERK waves produce feedback on one another
and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical
waves at both the local and global levels.
acknowledgement: We thank all members of the Hannezo group for discussions and suggestions,
as well as Sound Wai Phow for technical assistance. This work received funding from
the European Research Council under the EU Horizon 2020 research and innovation
program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and
the Ministry of Education under the Research Centres of Excellence program through
the MBI at NUS.
article_number: '013001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning
and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001
apa: Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between
mechanochemical patterning and glassy dynamics in cellular monolayers. PRX
Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001
chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay
between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.”
PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.
ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers,” PRX Life, vol.
1, no. 1. American Physical Society, 2023.
ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.
mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and
Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001,
American Physical Society, 2023, doi:10.1103/prxlife.1.013001.
short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).
date_created: 2023-09-06T08:30:59Z
date_published: 2023-07-20T00:00:00Z
date_updated: 2023-09-15T06:39:17Z
day: '20'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1103/prxlife.1.013001
ec_funded: 1
file:
- access_level: open_access
checksum: f881d98c89eb9f1aa136d7b781511553
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:30:50Z
date_updated: 2023-09-15T06:30:50Z
file_id: '14335'
file_name: 2023_PRXLife_Boocock.pdf
file_size: 2559520
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:30:50Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: PRX Life
publication_identifier:
issn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Interplay between mechanochemical patterning and glassy dynamics in cellular
monolayers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2023'
...
---
_id: '14314'
abstract:
- lang: eng
text: The execution of cognitive functions requires coordinated circuit activity
across different brain areas that involves the associated firing of neuronal assemblies.
Here, we tested the circuit mechanism behind assembly interactions between the
hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording
neuronal populations during a rule-switching task. We identified functionally
coupled CA1-mPFC cells that synchronized their activity beyond that expected from
common spatial coding or oscillatory firing. When such cell pairs fired together,
the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent
theta firing phases, independent of the theta timing of their CA1 counterpart.
These functionally connected CA1-mPFC cells formed interconnected assemblies.
While firing together with their CA1 assembly partners, mPFC cells fired along
specific theta sequences. Our results suggest that upregulated theta oscillatory
firing of mPFC cells can signal transient interactions with specific CA1 assemblies,
thus enabling distributed computations.
acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on
an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS
(grant 607616).
article_number: '113015'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports.
2023;42(9). doi:10.1016/j.celrep.2023.113015
apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations
as a substrate for medial prefrontal-hippocampal assembly interactions. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015
chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari.
“Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly
Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.
ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as
a substrate for medial prefrontal-hippocampal assembly interactions,” Cell
Reports, vol. 42, no. 9. Elsevier, 2023.
ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9),
113015.
mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal
Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier,
2023, doi:10.1016/j.celrep.2023.113015.
short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2023-09-15T07:14:12Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2023.113015
ec_funded: 1
external_id:
pmid:
- '37632747'
file:
- access_level: open_access
checksum: ca77a304fb813c292550b8604b0fb41d
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T07:12:46Z
date_updated: 2023-09-15T07:12:46Z
file_id: '14337'
file_name: 2023_CellPress_Nardin.pdf
file_size: 4879455
relation: main_file
success: 1
file_date_updated: 2023-09-15T07:12:46Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: Inter-and intracellular signalling in schizophrenia
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14315'
abstract:
- lang: eng
text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly
demolish the nuclear pore complex. However, for poorly understood reasons, caspases
are also activated during cell differentiation. Here, we show that sublethal activation
of caspases during myogenesis results in the transient proteolysis of four peripheral
Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective,
and we identified in an unbiased manner several classes of cytoplasmic, plasma
membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC
trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic
reticulum stress. Our results suggest that caspases can reversibly modulate nuclear
transport activity, which allows them to function as agents of cell differentiation
and adaptation at sublethal levels.
acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk),
Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital)
for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin
(Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto
and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra
Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing
mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical
Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH),
and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC).
This work was also supported by the Mass Spectrometry Core of the Salk Institute
with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine.
We thank Jolene Diedrich and Antonio Pinto for technical support.'
article_number: RP89066
article_processing_charge: Yes
article_type: original
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- 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: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation
and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066
apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex
trimming in cell differentiation and endoplasmic reticulum stress. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.89066
chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex
Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife.
eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.
ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12.
eLife Sciences Publications, 2023.
ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.
mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming
in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol.
12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.
short: U.H. Cho, M. Hetzer, ELife 12 (2023).
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-04T00:00:00Z
date_updated: 2023-09-15T07:07:10Z
day: '04'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.7554/eLife.89066
external_id:
pmid:
- '37665327'
file:
- access_level: open_access
checksum: db24bf3d595507387b48d3799c33e289
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:59:10Z
date_updated: 2023-09-15T06:59:10Z
file_id: '14336'
file_name: 2023_eLife_Cho.pdf
file_size: 3703097
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:59:10Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Caspase-mediated nuclear pore complex trimming in cell differentiation and
endoplasmic reticulum stress
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '14319'
abstract:
- lang: eng
text: "We study multigraphs whose edge-sets are the union of three perfect matchings,
M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6
n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2
f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture
however that if G is bipartite, the same result holds with n - 2 replaced by n
- 1. We give a construction that shows such a result would be tight. We\r\nalso
make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."
acknowledgement: Anastos has received funding from the European Union’s Horizon 2020
research and in-novation programme under the Marie Sk lodowska-Curie grant agreement
No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft
(DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).
article_number: P3.10
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: David
full_name: Fabian, David
last_name: Fabian
- first_name: Alp
full_name: Müyesser, Alp
last_name: Müyesser
- first_name: Tibor
full_name: Szabó, Tibor
last_name: Szabó
citation:
ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein
conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3).
doi:10.37236/11714
apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings
and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of
Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714
chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting
Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.
ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and
the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics,
vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.
ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the
Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics.
30(3), P3.10.
mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture
for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10,
Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.
short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics
30 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-28T00:00:00Z
date_updated: 2023-09-15T08:12:30Z
day: '28'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/11714
ec_funded: 1
external_id:
arxiv:
- '2212.03100'
file:
- access_level: open_access
checksum: 52c46c8cb329f9aaee9ade01525f317b
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T08:02:09Z
date_updated: 2023-09-15T08:02:09Z
file_id: '14338'
file_name: 2023_elecJournCombinatorics_Anastos.pdf
file_size: 247917
relation: main_file
success: 1
file_date_updated: 2023-09-15T08:02:09Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
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: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '14318'
abstract:
- lang: eng
text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing
the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider
the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime
T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims
at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem,
the classical and most well-known approach is the cookbook method by Karp (JACM
1994), while other approaches are mostly limited to deriving tail bounds of specific
PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach
for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing
time and random passed sizes observe discrete or (piecewise) uniform distribution
and whose recursive call is either a single procedure call or a divide-and-conquer.
We first establish a theoretical approach via Markov’s inequality, and then instantiate
the theoretical approach with a template-based algorithmic approach via a refined
treatment of exponentiation. Experimental evaluation shows that our algorithmic
approach is capable of deriving tail bounds that are (i) asymptotically tighter
than Karp’s method, (ii) match the best-known manually-derived asymptotic tail
bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor)
than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover,
our algorithmic approach handles all examples (including realistic PRRs such as
QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing
that our approach is efficient in practice."
acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential
theory of reals. The work is partially supported by the National Natural Science
Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt),
the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa
Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic
recurrence relations. In: Computer Aided Verification. Vol 13966. Springer
Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2'
apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated
tail bound analysis for probabilistic recurrence relations. In Computer Aided
Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2'
chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady.
“Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer
Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.
ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound
analysis for probabilistic recurrence relations,” in Computer Aided Verification,
Paris, France, 2023, vol. 13966, pp. 16–39.
ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis
for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer
Aided Verification, LNCS, vol. 13966, 16–39.'
mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence
Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023,
pp. 16–39, doi:10.1007/978-3-031-37709-9_2.
short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 16–39.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-20T08:25:57Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_2
ec_funded: 1
file:
- access_level: open_access
checksum: 42917e086f8c7699f3bccf84f74fe000
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:24:47Z
date_updated: 2023-09-20T08:24:47Z
file_id: '14348'
file_name: 2023_LNCS_Sun.pdf
file_size: 624647
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:24:47Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16-39
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/boyvolcano/PRR
scopus_import: '1'
status: public
title: Automated tail bound analysis for probabilistic recurrence relations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14317'
abstract:
- lang: eng
text: "Markov decision processes can be viewed as transformers of probability distributions.
While this view is useful from a practical standpoint to reason about trajectories
of distributions, basic reachability and safety problems are known to be computationally
intractable (i.e., Skolem-hard) to solve in such models. Further, we show that
even for simple examples of MDPs, strategies for safety objectives over distributions
can require infinite memory and randomization.\r\nIn light of this, we present
a novel overapproximation approach to synthesize strategies in an MDP, such that
a safety objective over the distributions is met. More precisely, we develop a
new framework for template-based synthesis of certificates as affine distributional
and inductive invariants for safety objectives in MDPs. We provide two algorithms
within this framework. One can only synthesize memoryless strategies, but has
relative completeness guarantees, while the other can synthesize general strategies.
The runtime complexity of both algorithms is in PSPACE. We implement these algorithms
and show that they can solve several non-trivial examples."
acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt)
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project
EQuaVE and SERB Matrices grant MTR/2018/00074.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: S.
full_name: Akshay, S.
last_name: Akshay
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers:
Affine invariant synthesis for safety objectives. In: International Conference
on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5'
apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs
as distribution transformers: Affine invariant synthesis for safety objectives.
In International Conference on Computer Aided Verification (Vol. 13966,
pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5'
chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic.
“MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.”
In International Conference on Computer Aided Verification, 13966:86–112.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.'
ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution
transformers: Affine invariant synthesis for safety objectives,” in International
Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966,
pp. 86–112.'
ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution
transformers: Affine invariant synthesis for safety objectives. International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13966, 86–112.'
mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis
for Safety Objectives.” International Conference on Computer Aided Verification,
vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.'
short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International
Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2023-09-20T09:04:40Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_5
ec_funded: 1
file:
- access_level: open_access
checksum: f143c8eedf609f20f2aad2eeb496d53f
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:46:43Z
date_updated: 2023-09-20T08:46:43Z
file_id: '14349'
file_name: 2023_LNCS_Akshay.pdf
file_size: 531745
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:46:43Z
has_accepted_license: '1'
intvolume: ' 13966'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 86-112
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13966
year: '2023'
...
---
_id: '14316'
abstract:
- lang: eng
text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport.
In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted
to generate distinct transport vesicles at the trans-Golgi network (TGN), and
the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories
for these adaptors. Recently, we showed that vesicle transport from the TGN is
crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p
are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However,
these observations were incompatible with previous studies showing that these
adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall
mechanism responsible for regulation of Vps21p activity remains ambiguous. Here,
we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated
Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired
transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to
the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA
adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and
Ypt32p were found to have partially overlapping functions for recruitment of AP-1
and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors
for Vps21p activation in the TGN–endosome trafficking pathway.
article_number: jcs261448
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Hiroki
full_name: Shimamura, Hiroki
last_name: Shimamura
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct
role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448
apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &
Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p
activation in the TGN-endosome trafficking pathway. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.261448
chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko
Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors
for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of
Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.
ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J.
Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation
in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol.
136, no. 17. The Company of Biologists, 2023.
ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023.
Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 136(17), jcs261448.
mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for
Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell
Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.
short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima,
Journal of Cell Science 136 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-09-20T09:14:15Z
day: '01'
department:
- _id: DaSi
doi: 10.1242/jcs.261448
external_id:
pmid:
- '37539494'
intvolume: ' 136'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.27.534325
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the
TGN-endosome trafficking pathway
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '14320'
abstract:
- lang: eng
text: The development of two-dimensional materials has resulted in a diverse range
of novel, high-quality compounds with increasing complexity. A key requirement
for a comprehensive quantitative theory is the accurate determination of these
materials' band structure parameters. However, this task is challenging due to
the intricate band structures and the indirect nature of experimental probes.
In this work, we introduce a general framework to derive band structure parameters
from experimental data using deep neural networks. We applied our method to the
penetration field capacitance measurement of trilayer graphene, an effective probe
of its density of states. First, we demonstrate that a trained deep network gives
accurate predictions for the penetration field capacitance as a function of tight-binding
parameters. Next, we use the fast and accurate predictions from the trained network
to automatically determine tight-binding parameters directly from experimental
data, with extracted parameters being in a good agreement with values in the literature.
We conclude by discussing potential applications of our method to other materials
and experimental techniques beyond penetration field capacitance.
acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy
under award DE-SC0020043, and additional support from the Gordon and Betty Moore
Foundation under award GBMF9471 for group operations.
article_number: '125411'
article_processing_charge: No
article_type: original
author:
- first_name: Paul M
full_name: Henderson, Paul M
id: 13C09E74-18D9-11E9-8878-32CFE5697425
last_name: Henderson
orcid: 0000-0002-5198-7445
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Alexander A.
full_name: Zibrov, Alexander A.
last_name: Zibrov
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction
of band structure parameters from density of states: A case study on trilayer
graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411'
apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn,
M. (2023). Deep learning extraction of band structure parameters from density
of states: A case study on trilayer graphene. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.108.125411'
chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young,
and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from
Density of States: A Case Study on Trilayer Graphene.” Physical Review B.
American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.'
ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn,
“Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12.
American Physical Society, 2023.'
ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning
extraction of band structure parameters from density of states: A case study on
trilayer graphene. Physical Review B. 108(12), 125411.'
mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters
from Density of States: A Case Study on Trilayer Graphene.” Physical Review
B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.'
short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical
Review B 108 (2023).
date_created: 2023-09-12T07:12:12Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-09-20T09:38:24Z
day: '15'
department:
- _id: MaSe
- _id: ChLa
- _id: MiLe
doi: 10.1103/physrevb.108.125411
external_id:
arxiv:
- '2210.06310'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.06310
month: '09'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deep learning extraction of band structure parameters from density of states:
A case study on trilayer graphene'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '12732'
abstract:
- lang: eng
text: "Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize,
provide a fascinating research direction both for fundamental reasons and for
application in state of the art quantum devices.\r\nGoing beyond the description
of statistical mechanics, ergodicity breaking yields a new paradigm in quantum
many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn
this Thesis, we address different open questions in the field, focusing on disorder-induced
many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained
models.\r\nIn particular, we contribute to the debate about transport in kinetically
constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry
breaking in a family of quantum East models.\r\nUsing tensor network techniques,
we analyze the dynamics of large MBL systems beyond the limit of exact numerical
methods.\r\nIn this setting, we approach the debated topic of the coexistence
of localized and thermal eigenstates separated by energy thresholds known as many-body
mobility edges.\r\nInspired by recent experiments, our work further investigates
the localization of a small bath induced by the coupling to a large localized
chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce
a family of particle-conserving kinetically constrained models, inspired by the
quantum East model.\r\nThe system we study features strong inversion-symmetry
breaking, due to the nature of the correlated hopping.\r\nWe show that these models
host so-called quantum Hilbert space fragmentation, consisting of disconnected
subsectors in an entangled basis, and further provide an analytical description
of this phenomenon.\r\nWe further probe its effect on dynamics of simple product
states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics
within the largest subsector reveals an anomalous transient superdiffusive behavior
crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests
that particle conserving constrained models with inversion-symmetry breaking realize
new universality classes of dynamics and invite their further theoretical and
experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to
design a model with many-body mobility edges in particle density.\r\nThis feature
allows to study the dynamics of localized and thermal states in large systems
beyond the limitations of previous studies.\r\nThe time-evolution shows typical
signatures of localization at small densities, replaced by thermal behavior at
larger densities.\r\nOur results provide evidence in favor of the stability of
many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo
support our findings, we probe the mechanism proposed as a cause of delocalization
in many-body localized systems with mobility edges suggesting its ineffectiveness
in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the
topic of many-body localization proximity effect.\r\nWe study a model inspired
by recent experiments, featuring Anderson localized coupled to a small bath of
free hard-core bosons.\r\nThe interaction among the two particle species results
in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur
simulations show convincing evidence of many-body localization proximity effect
when the bath is composed by a single free particle and interactions are strong.\r\nWe
furthter observe an anomalous entanglement dynamics, which we explain through
a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of
large systems, providing supplementary evidence in favor of our findings."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
citation:
ama: Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum
many-body systems. 2023. doi:10.15479/at:ista:12732
apa: Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732
chicago: Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:12732.
ieee: P. Brighi, “Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems,” Institute of Science and Technology Austria, 2023.
ista: Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained
quantum many-body systems. Institute of Science and Technology Austria.
mla: Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:12732.
short: P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained
Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-17T13:30:48Z
date_published: 2023-03-21T00:00:00Z
date_updated: 2023-09-20T10:44:12Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaSe
doi: 10.15479/at:ista:12732
ec_funded: 1
file:
- access_level: closed
checksum: 5d2de651ef9449c1b8dc27148ca74777
content_type: application/zip
creator: pbrighi
date_created: 2023-03-23T16:42:56Z
date_updated: 2023-03-23T16:42:56Z
file_id: '12753'
file_name: Thesis_sub_PBrighi.zip
file_size: 42167561
relation: source_file
- access_level: open_access
checksum: 7caa153d4a5b0873a79358787d2dfe1e
content_type: application/pdf
creator: pbrighi
date_created: 2023-03-23T16:43:14Z
date_updated: 2023-03-23T16:43:14Z
file_id: '12754'
file_name: Thesis_PBrighi.pdf
file_size: 13977000
relation: main_file
success: 1
file_date_updated: 2023-03-23T16:43:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: None
page: '158'
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11470'
relation: part_of_dissertation
status: public
- id: '8308'
relation: part_of_dissertation
status: public
- id: '11469'
relation: part_of_dissertation
status: public
- id: '12750'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
title: Ergodicity breaking in disordered and kinetically constrained quantum many-body
systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14334'
abstract:
- lang: eng
text: Quantum kinetically constrained models have recently attracted significant
attention due to their anomalous dynamics and thermalization. In this work, we
introduce a hitherto unexplored family of kinetically constrained models featuring
conserved particle number and strong inversion-symmetry breaking due to facilitated
hopping. We demonstrate that these models provide a generic example of so-called
quantum Hilbert space fragmentation, that is manifested in disconnected sectors
in the Hilbert space that are not apparent in the computational basis. Quantum
Hilbert space fragmentation leads to an exponential in system size number of eigenstates
with exactly zero entanglement entropy across several bipartite cuts. These eigenstates
can be probed dynamically using quenches from simple initial product states. In
addition, we study the particle spreading under unitary dynamics launched from
the domain wall state, and find faster than diffusive dynamics at high particle
densities, that crosses over into logarithmically slow relaxation at smaller densities.
Using a classically simulable cellular automaton, we reproduce the logarithmic
dynamics observed in the quantum case. Our work suggests that particle conserving
constrained models with inversion symmetry breaking realize so far unexplored
dynamical behavior and invite their further theoretical and experimental studies.
acknowledgement: "We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry
Abanin for useful\r\ndiscussions.The authors acknowledge support by the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger
International\r\nInstitute for Mathematics and Physics (ESI)."
article_number: '093'
article_processing_charge: No
article_type: original
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics
in particle-conserving quantum East models. SciPost Physics. 2023;15(3).
doi:10.21468/scipostphys.15.3.093
apa: Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation
and slow dynamics in particle-conserving quantum East models. SciPost Physics.
SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093
chicago: Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation
and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics.
SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.
ieee: P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models,” SciPost Physics,
vol. 15, no. 3. SciPost Foundation, 2023.
ista: Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow
dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.
mla: Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving
Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation,
2023, doi:10.21468/scipostphys.15.3.093.
short: P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).
date_created: 2023-09-14T13:08:23Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2023-09-20T10:46:29Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.15.3.093
ec_funded: 1
external_id:
arxiv:
- '2210.15607'
file:
- access_level: open_access
checksum: 4cef6a8021f6b6c47ab2f2f2b1387ac2
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T10:46:10Z
date_updated: 2023-09-20T10:46:10Z
file_id: '14350'
file_name: 2023_SciPostPhysics_Brighi.pdf
file_size: 4866506
relation: main_file
success: 1
file_date_updated: 2023-09-20T10:46:10Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
record:
- id: '12750'
relation: earlier_version
status: public
status: public
title: Hilbert space fragmentation and slow dynamics in particle-conserving quantum
East models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2023-09-20T09:48:12Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Achiral dipoles on a ferromagnet can affect its magnetization direction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2023'
...
---
_id: '14342'
abstract:
- lang: eng
text: We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared
frequency range that avoids using sophisticated infrared detectors. Our approach
is based on using a near-infrared probe beam which interacts with a mid-IR beam
via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring
XPM-induced spectral modifications in the probe beam and comparing the experimental
data with simulation results, we extract the value for the non-degenerate Kerr
index. Finally, in order to obtain the value of degenerate mid-IR Kerr index,
we use the well-established two-band formalism of Sheik-Bahae et al., which is
shown to become particularly simple in the limit of low frequencies. The proposed
technique is complementary to the conventional techniques, such as z-scan, and
has the advantage of not requiring any mid-infrared detectors.
acknowledgement: The work was supported by IST Austria. The authors would like to
gratefully acknowledge the help and assistance of Professor John M. Dudley.
article_number: '091104'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9).
doi:10.1063/5.0161713
apa: Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation
via cross-phase modulation with a near-infrared probe beam. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0161713
chicago: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.
ieee: D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam,” Applied Physics Letters, vol.
123, no. 9. AIP Publishing, 2023.
ista: Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase
modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.
mla: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation
via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics
Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.
short: D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).
date_created: 2023-09-17T22:01:09Z
date_published: 2023-08-28T00:00:00Z
date_updated: 2023-09-20T11:50:06Z
day: '28'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1063/5.0161713
external_id:
arxiv:
- '2306.09043'
file:
- access_level: open_access
checksum: 89a1b604d58b209fec66c6b6f919ac98
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T11:36:16Z
date_updated: 2023-09-20T11:36:16Z
file_id: '14353'
file_name: 2023_ApplPhysLetter_Lorenc.pdf
file_size: 1486715
relation: main_file
success: 1
file_date_updated: 2023-09-20T11:36:16Z
has_accepted_license: '1'
intvolume: ' 123'
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared
probe beam
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2023'
...
---
_id: '13120'
abstract:
- lang: eng
text: 'We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant.
We defined basic notions of rewrite rules and of words derived by a grammar, and
used grammars to show closure of the class of type-0 languages under four operations:
union, reversal, concatenation, and the Kleene star. The literature mostly focuses
on Turing machine arguments, which are possibly more difficult to formalize. For
the Kleene star, we could not follow the literature and came up with our own grammar-based
construction.'
acknowledgement: "Jasmin Blanchette: This research has received funding from the Netherlands
Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No.
016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making
this collaboration possible. We\r\nthank Václav Končický for discussing ideas about
the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano
Testa for their small yet very valuable contributions to our code. We thank Eric
Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting
textual improvements. We thank the anonymous reviewers for very helpful comments.
Finally, we thank the Lean community for helping us with various technical issues
and answering many questions. "
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: No
author:
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
- first_name: Jasmin
full_name: Blanchette, Jasmin
last_name: Blanchette
citation:
ama: 'Dvorak M, Blanchette J. Closure properties of general grammars - formally
verified. In: 14th International Conference on Interactive Theorem Proving.
Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15'
apa: 'Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars
- formally verified. In 14th International Conference on Interactive Theorem
Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15'
chicago: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars
- Formally Verified.” In 14th International Conference on Interactive Theorem
Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
https://doi.org/10.4230/LIPIcs.ITP.2023.15.
ieee: M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally
verified,” in 14th International Conference on Interactive Theorem Proving,
Bialystok, Poland, 2023, vol. 268.
ista: 'Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally
verified. 14th International Conference on Interactive Theorem Proving. ITP: International
Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.'
mla: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars
- Formally Verified.” 14th International Conference on Interactive Theorem
Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ITP.2023.15.
short: M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive
Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-08-04
location: Bialystok, Poland
name: 'ITP: International Conference on Interactive Theorem Proving'
start_date: 2023-07-31
date_created: 2023-06-05T07:29:05Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-09-25T11:04:29Z
day: '27'
ddc:
- '000'
department:
- _id: GradSch
- _id: VlKo
doi: 10.4230/LIPIcs.ITP.2023.15
external_id:
arxiv:
- '2302.06420'
file:
- access_level: open_access
checksum: 773a0197f05b67feaa6cb1e17ec3642d
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T11:55:43Z
date_updated: 2023-08-07T11:55:43Z
file_id: '13982'
file_name: 2023_LIPIcS_Dvorak.pdf
file_size: 715976
relation: main_file
success: 1
file_date_updated: 2023-08-07T11:55:43Z
has_accepted_license: '1'
intvolume: ' 268'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 14th International Conference on Interactive Theorem Proving
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772846'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/madvorak/grammars/tree/publish
scopus_import: '1'
status: public
title: Closure properties of general grammars - formally verified
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 268
year: '2023'
...
---
_id: '13969'
abstract:
- lang: eng
text: "Bundling crossings is a strategy which can enhance the readability\r\nof
graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany
two edges have at most one common point which can be a common vertex or a\r\ncrossing.
Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation
of the bundled crossing number of a good drawing with no toothed\r\nhole. In general
the number of toothed holes has to be added to the 8-approximation.\r\nIn the
special case of circular drawings the approximation factor is 8, this improves\r\nupon
the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation
factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce.
We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe
pseudosegments is bipartite and has no toothed hole."
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1. An extended abstract of this paper has been published in
the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.
article_processing_charge: Yes
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal
of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629
apa: Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled
crossing number. Journal of Graph Algorithms and Applications. Brown University.
https://doi.org/10.7155/jgaa.00629
chicago: Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” Journal of Graph Algorithms and Applications. Brown University,
2023. https://doi.org/10.7155/jgaa.00629.
ieee: A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,”
Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University,
pp. 433–457, 2023.
ista: Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number.
Journal of Graph Algorithms and Applications. 27(6), 433–457.
mla: Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6,
Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629.
short: A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications
27 (2023) 433–457.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-09-25T10:56:10Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.7155/jgaa.00629
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
file:
- access_level: open_access
checksum: 9c30d2b8e324cc1c904f2aeec92013a3
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T08:00:48Z
date_updated: 2023-08-07T08:00:48Z
file_id: '13979'
file_name: 2023_JourGraphAlgorithms_Arroyo.pdf
file_size: 865774
relation: main_file
success: 1
file_date_updated: 2023-08-07T08:00:48Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 433-457
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Graph Algorithms and Applications
publication_identifier:
issn:
- 1526-1719
publication_status: published
publisher: Brown University
quality_controlled: '1'
related_material:
record:
- id: '11185'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Approximating the bundled crossing number
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2023'
...
---
_id: '14344'
abstract:
- lang: eng
text: We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in
two different settings. In the first one, G is given to us in the form of randomly
ordered adjacency lists while in the second one, we are given the adjacency matrix
of G. In each of the two settings we derive a deterministic algorithm that w.h.p.
either finds a Hamilton cycle or returns a certificate that such a cycle does
not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively,
each being best possible in its own setting.
article_processing_charge: No
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: 'Anastos M. Fast algorithms for solving the Hamilton cycle problem with high
probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88'
apa: 'Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem
with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88'
chicago: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem
with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on
Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics,
2023. https://doi.org/10.1137/1.9781611977554.ch88.
ieee: M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high
probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms,
Florence, Italy, 2023, vol. 2023, pp. 2286–2323.
ista: 'Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with
high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.'
mla: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with
High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023,
pp. 2286–323, doi:10.1137/1.9781611977554.ch88.
short: M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete
Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
date_created: 2023-09-17T22:01:10Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-25T09:13:41Z
day: '01'
department:
- _id: MaKw
doi: 10.1137/1.9781611977554.ch88
external_id:
arxiv:
- '2111.14759'
intvolume: ' 2023'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.14759
month: '01'
oa: 1
oa_version: Preprint
page: 2286-2323
publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast algorithms for solving the Hamilton cycle problem with high probability
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2023
year: '2023'
...
---
_id: '12710'
abstract:
- lang: eng
text: Surface curvature both emerges from, and influences the behavior of, living
objects at length scales ranging from cell membranes to single cells to tissues
and organs. The relevance of surface curvature in biology is supported by numerous
experimental and theoretical investigations in recent years. In this review, first,
a brief introduction to the key ideas of surface curvature in the context of biological
systems is given and the challenges that arise when measuring surface curvature
are discussed. Giving an overview of the emergence of curvature in biological
systems, its significance at different length scales becomes apparent. On the
other hand, summarizing current findings also shows that both single cells and
entire cell sheets, tissues or organisms respond to curvature by modulating their
shape and their migration behavior. Finally, the interplay between the distribution
of morphogens or micro-organisms and the emergence of curvature across length
scales is addressed with examples demonstrating these key mechanistic principles
of morphogenesis. Overall, this review highlights that curved interfaces are not
merely a passive by-product of the chemical, biological, and mechanical processes
but that curvature acts also as a signal that co-determines these processes.
acknowledgement: B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F.
acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through
IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from
Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD.
A.S. acknowledges that this work was partially supported by the ATTRACT Investigator
Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research
Fund. The author thanks Gerardo Ceada for his help in the graphical representations.
N.A.K. acknowledges support from the European Research Council (grant 851960) and
the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands
Organization for Scientific Research (024.003.013). M.B.A. acknowledges support
from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project
“Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through
project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft
(DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation
(PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.
article_number: '2206110'
article_processing_charge: No
article_type: review
author:
- first_name: Barbara
full_name: Schamberger, Barbara
last_name: Schamberger
- first_name: Ricardo
full_name: Ziege, Ricardo
last_name: Ziege
- first_name: Karine
full_name: Anselme, Karine
last_name: Anselme
- first_name: Martine
full_name: Ben Amar, Martine
last_name: Ben Amar
- first_name: Michał
full_name: Bykowski, Michał
last_name: Bykowski
- first_name: André P.G.
full_name: Castro, André P.G.
last_name: Castro
- first_name: Amaia
full_name: Cipitria, Amaia
last_name: Cipitria
- first_name: Rhoslyn A.
full_name: Coles, Rhoslyn A.
last_name: Coles
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Michaela
full_name: Eder, Michaela
last_name: Eder
- first_name: Sebastian
full_name: Ehrig, Sebastian
last_name: Ehrig
- first_name: Luis M.
full_name: Escudero, Luis M.
last_name: Escudero
- first_name: Myfanwy E.
full_name: Evans, Myfanwy E.
last_name: Evans
- first_name: Paulo R.
full_name: Fernandes, Paulo R.
last_name: Fernandes
- first_name: Peter
full_name: Fratzl, Peter
last_name: Fratzl
- first_name: Liesbet
full_name: Geris, Liesbet
last_name: Geris
- first_name: Notburga
full_name: Gierlinger, Notburga
last_name: Gierlinger
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Aleš
full_name: Iglič, Aleš
last_name: Iglič
- first_name: Jacob J.K.
full_name: Kirkensgaard, Jacob J.K.
last_name: Kirkensgaard
- first_name: Philip
full_name: Kollmannsberger, Philip
last_name: Kollmannsberger
- first_name: Łucja
full_name: Kowalewska, Łucja
last_name: Kowalewska
- first_name: Nicholas A.
full_name: Kurniawan, Nicholas A.
last_name: Kurniawan
- first_name: Ioannis
full_name: Papantoniou, Ioannis
last_name: Papantoniou
- first_name: Laurent
full_name: Pieuchot, Laurent
last_name: Pieuchot
- first_name: Tiago H.V.
full_name: Pires, Tiago H.V.
last_name: Pires
- first_name: Lars D.
full_name: Renner, Lars D.
last_name: Renner
- first_name: Andrew O.
full_name: Sageman-Furnas, Andrew O.
last_name: Sageman-Furnas
- first_name: Gerd E.
full_name: Schröder-Turk, Gerd E.
last_name: Schröder-Turk
- first_name: Anupam
full_name: Sengupta, Anupam
last_name: Sengupta
- first_name: Vikas R.
full_name: Sharma, Vikas R.
last_name: Sharma
- first_name: Antonio
full_name: Tagua, Antonio
last_name: Tagua
- first_name: Caterina
full_name: Tomba, Caterina
last_name: Tomba
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Sarah L.
full_name: Waters, Sarah L.
last_name: Waters
- first_name: Edwina F.
full_name: Yeo, Edwina F.
last_name: Yeo
- first_name: Andreas
full_name: Roschger, Andreas
last_name: Roschger
- first_name: Cécile M.
full_name: Bidan, Cécile M.
last_name: Bidan
- first_name: John W.C.
full_name: Dunlop, John W.C.
last_name: Dunlop
citation:
ama: 'Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems:
Its quantification, emergence, and implications across the scales. Advanced
Materials. 2023;35(13). doi:10.1002/adma.202206110'
apa: 'Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro,
A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification,
emergence, and implications across the scales. Advanced Materials. Wiley.
https://doi.org/10.1002/adma.202206110'
chicago: 'Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar,
Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological
Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced
Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.'
ieee: 'B. Schamberger et al., “Curvature in biological systems: Its quantification,
emergence, and implications across the scales,” Advanced Materials, vol.
35, no. 13. Wiley, 2023.'
ista: 'Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria
A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl
P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger
P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD,
Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C,
Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature
in biological systems: Its quantification, emergence, and implications across
the scales. Advanced Materials. 35(13), 2206110.'
mla: 'Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification,
Emergence, and Implications across the Scales.” Advanced Materials, vol.
35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.'
short: B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro,
A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans,
P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K.
Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou,
L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk,
A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo,
A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).
date_created: 2023-03-05T23:01:06Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2023-09-26T10:56:46Z
day: '29'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1002/adma.202206110
external_id:
isi:
- '000941068900001'
pmid:
- '36461812'
file:
- access_level: open_access
checksum: 5c04d68130e97a0ecd1ca27fbc15a246
content_type: application/pdf
creator: dernst
date_created: 2023-09-26T10:51:56Z
date_updated: 2023-09-26T10:51:56Z
file_id: '14373'
file_name: 2023_AdvancedMaterials_Schamberger.pdf
file_size: 2898063
relation: main_file
success: 1
file_date_updated: 2023-09-26T10:51:56Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Curvature in biological systems: Its quantification, emergence, and implications
across the scales'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '13340'
abstract:
- lang: eng
text: Photoisomerization of azobenzenes from their stable E isomer to the metastable
Z state is the basis of numerous applications of these molecules. However, this
reaction typically requires ultraviolet light, which limits applicability. In
this study, we introduce disequilibration by sensitization under confinement (DESC),
a supramolecular approach to induce the E-to-Z isomerization by using light of
a desired color, including red. DESC relies on a combination of a macrocyclic
host and a photosensitizer, which act together to selectively bind and sensitize
E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is
expelled from the host, which can then convert additional E-azobenzenes to the
Z state. In this way, the host–photosensitizer complex converts photon energy
into chemical energy in the form of out-of-equilibrium photostationary states,
including ones that cannot be accessed through direct photoexcitation.
acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research
and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223
(A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)],
the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.),
Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant
340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s
PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1
(M.J.F.)].
article_processing_charge: No
article_type: original
author:
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Jonathan R.
full_name: Church, Jonathan R.
last_name: Church
- first_name: Tero-Petri
full_name: Ruoko, Tero-Petri
last_name: Ruoko
- first_name: Nikita
full_name: Durandin, Nikita
last_name: Durandin
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Maren
full_name: Weissenfels, Maren
last_name: Weissenfels
- first_name: Moran
full_name: Feller, Moran
last_name: Feller
- first_name: Miri
full_name: Kazes, Miri
last_name: Kazes
- first_name: Veniamin A.
full_name: Borin, Veniamin A.
last_name: Borin
- first_name: Magdalena
full_name: Odaybat, Magdalena
last_name: Odaybat
- first_name: Rishir
full_name: Kalepu, Rishir
last_name: Kalepu
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Dan
full_name: Oron, Dan
last_name: Oron
- first_name: Matthew J.
full_name: Fuchter, Matthew J.
last_name: Fuchter
- first_name: Arri
full_name: Priimagi, Arri
last_name: Priimagi
- first_name: Igor
full_name: Schapiro, Igor
last_name: Schapiro
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light
sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059
apa: Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels,
M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization
under confinement. Science. American Association for the Advancement of
Science. https://doi.org/10.1126/science.adh9059
chicago: Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał
J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes
by Visible-Light Sensitization under Confinement.” Science. American Association
for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059.
ieee: J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization
under confinement,” Science, vol. 381, no. 6664. American Association for
the Advancement of Science, pp. 1357–1363, 2023.
ista: Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller
M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ,
Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light
sensitization under confinement. Science. 381(6664), 1357–1363.
mla: Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization
under Confinement.” Science, vol. 381, no. 6664, American Association for
the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.
short: J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels,
M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron,
M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.
date_created: 2023-08-01T08:26:15Z
date_published: 2023-09-22T00:00:00Z
date_updated: 2023-10-03T08:11:26Z
day: '22'
department:
- _id: RaKl
doi: 10.1126/science.adh9059
intvolume: ' 381'
issue: '6664'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv-2023-gq2h0
month: '09'
oa: 1
oa_version: Preprint
page: 1357-1363
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disequilibrating azoarenes by visible-light sensitization under confinement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...