---
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-31T00:00:00Z
date_updated: 2024-02-21T12:18:18Z
day: '31'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
isi:
- '001065254200001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41587-023-01911-8
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/CATS
record:
- id: '13126'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Imaging brain tissue architecture across millimeter to nanometer scales
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14258'
abstract:
- lang: eng
text: There is currently little evidence that the genetic basis of human phenotype
varies significantly across the lifespan. However, time-to-event phenotypes are
understudied and can be thought of as reflecting an underlying hazard, which is
unlikely to be constant through life when values take a broad range. Here, we
find that 74% of 245 genome-wide significant genetic associations with age at
natural menopause (ANM) in the UK Biobank show a form of age-specific effect.
Nineteen of these replicated discoveries are identified only by our modeling framework,
which determines the time dependency of DNA-variant age-at-onset associations
without a significant multiple-testing burden. Across the range of early to late
menopause, we find evidence for significantly different underlying biological
pathways, changes in the signs of genetic correlations of ANM to health indicators
and outcomes, and differences in inferred causal relationships. We find that DNA
damage response processes only act to shape ovarian reserve and depletion for
women of early ANM. Genetically mediated delays in ANM were associated with increased
relative risk of breast cancer and leiomyoma at all ages and with high cholesterol
and heart failure for late-ANM women. These findings suggest that a better understanding
of the age dependency of genetic risk factor relationships among health indicators
and outcomes is achievable through appropriate statistical modeling of large-scale
biobank data.
acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181)
and by core funding from the Institute of Science and Technology Austria. K.L. and
R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank
computations were performed in the High-Performance Computing Center, University
of Tartu. We thank Triin Laisk for her valuable insights and comments that helped
greatly. We would like to acknowledge the participants and investigators of UK Biobank
and Estonian Biobank studies. This project uses UK Biobank data under project number
35520.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Liza
full_name: Darrous, Liza
last_name: Darrous
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Kristi
full_name: Läll, Kristi
last_name: Läll
- first_name: Krista
full_name: Fischer, Krista
last_name: Fischer
- first_name: Reedik
full_name: Mägi, Reedik
last_name: Mägi
- first_name: Zoltan
full_name: Kutalik, Zoltan
last_name: Kutalik
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific
biological mechanisms governing human ovarian aging. American Journal of Human
Genetics. 2023;110(9):1549-1563. doi:10.1016/j.ajhg.2023.07.006
apa: Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., …
Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms
governing human ovarian aging. American Journal of Human Genetics. Elsevier.
https://doi.org/10.1016/j.ajhg.2023.07.006
chicago: Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer,
Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into
the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American
Journal of Human Genetics. Elsevier, 2023. https://doi.org/10.1016/j.ajhg.2023.07.006.
ieee: S. E. Ojavee et al., “Genetic insights into the age-specific biological
mechanisms governing human ovarian aging,” American Journal of Human Genetics,
vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.
ista: Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson
MR. 2023. Genetic insights into the age-specific biological mechanisms governing
human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.
mla: Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological
Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics,
vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:10.1016/j.ajhg.2023.07.006.
short: S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik,
M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.
date_created: 2023-09-03T22:01:15Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2024-01-30T13:21:05Z
day: '07'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2023.07.006
external_id:
pmid:
- '37543033'
file:
- access_level: open_access
checksum: 4108b031dc726ae6b4a5ae7e021ba188
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T13:20:35Z
date_updated: 2024-01-30T13:20:35Z
file_id: '14912'
file_name: 2023_AJHG_Ojavee.pdf
file_size: 2551276
relation: main_file
success: 1
file_date_updated: 2024-01-30T13:20:35Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 1549-1563
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic insights into the age-specific biological mechanisms governing human
ovarian aging
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: 110
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: '14260'
abstract:
- lang: eng
text: "This paper presents Lincheck, a new practical and user-friendly framework
for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck
provides a simple and declarative way to write concurrent tests: instead of describing
how to perform the test, users specify what to test by declaring all the operations
to examine; the framework automatically handles the rest. As a result, tests written
with Lincheck are concise and easy to understand. The framework automatically
generates a set of concurrent scenarios, examines them using stress-testing or
bounded model checking, and verifies that the results of each invocation are correct.
Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow
trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo
the best of our knowledge, Lincheck is the first production-ready tool on the
JVM that offers such a simple way of writing concurrent tests, without requiring
special skills or expertise. We successfully integrated Lincheck in the development
process of several large projects, such as Kotlin Coroutines, and identified new
bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque
and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is
used in most of the synchronization primitives. We believe that Lincheck can significantly
improve the quality and productivity of concurrent algorithms research and development
and become the state-of-the-art tool for checking their correctness."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Maria
full_name: Sokolova, Maria
last_name: Sokolova
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. In: 35th International
Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169.
doi:10.1007/978-3-031-37706-8_8'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. In 35th International Conference on Computer Aided Verification
(Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” In 35th International Conference on Computer Aided Verification
, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM,” in 35th
International Conference on Computer Aided Verification , Paris, France, 2023,
vol. 13964, pp. 156–169.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM. 35th International
Conference on Computer Aided Verification . CAV: Computer Aided Verification,
LNCS, vol. 13964, 156–169.'
mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM.” 35th International Conference on Computer Aided Verification
, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th
International Conference on Computer Aided Verification , Springer Nature, 2023,
pp. 156–169.
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: 2024-02-27T07:46:52Z
day: '17'
ddc:
- '000'
department:
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- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
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date_created: 2023-09-06T08:16:25Z
date_updated: 2023-09-06T08:16:25Z
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oa: 1
oa_version: Published Version
page: 156-169
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'
related_material:
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- id: '14995'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on JVM'
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: '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: '14274'
abstract:
- lang: eng
text: Immune responses rely on the rapid and coordinated migration of leukocytes.
Whereas it is well established that single-cell migration is often guided by gradients
of chemokines and other chemoattractants, it remains poorly understood how these
gradients are generated, maintained, and modulated. By combining experimental
data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor
(GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor
that steers migration, CCR7 also acts as a generator and a modulator of chemotactic
gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively
internalize the receptor and ligand as part of the canonical GPCR desensitization
response. We show that CCR7 internalization also acts as an effective sink for
the chemoattractant, dynamically shaping the spatiotemporal distribution of the
chemokine. This mechanism drives complex collective migration patterns, enabling
DCs to create or sharpen chemotactic gradients. We further show that these self-generated
gradients can sustain the long-range guidance of DCs, adapt collective migration
patterns to the size and geometry of the environment, and provide a guidance cue
for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses
and consumes its ligand can thus provide a novel mode of cellular self-organization.
acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences,
Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute
of Science and Technology Austria for excellent support, as well as all the rotation
students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis
work was supported by grants from the European Research Council under the European
Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant
agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20)
to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research
Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U.
was supported by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement no. 754411."
article_number: adc9584
article_processing_charge: No
article_type: original
author:
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- 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: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration. Science Immunology.
2023;8(87). doi:10.1126/sciimmunol.adc9584
apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin,
J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate
collective leukocyte migration. Science Immunology. American Association
for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584
chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz,
Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science
Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.
ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration,” Science Immunology, vol.
8, no. 87. American Association for the Advancement of Science, 2023.
ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB,
Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective
leukocyte migration. Science Immunology. 8(87), adc9584.
mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to
Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8,
no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.
short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B.
Hannezo, M.K. Sixt, Science Immunology 8 (2023).
date_created: 2023-09-06T08:07:51Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-12-21T14:30:01Z
day: '01'
department:
- _id: MiSi
- _id: EdHa
- _id: NanoFab
doi: 10.1126/sciimmunol.adc9584
ec_funded: 1
external_id:
isi:
- '001062110600003'
pmid:
- '37656776'
intvolume: ' 8'
isi: 1
issue: '87'
keyword:
- General Medicine
- Immunology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciimmunol.adc9584
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Science Immunology
publication_identifier:
issn:
- 2470-9468
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14279'
relation: research_data
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte
migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
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: '14279'
abstract:
- lang: eng
text: "The zip file includes source data used in the manuscript \"CCR7 acts as both
a sensor and a sink for CCL19 to coordinate collective leukocyte migration\",
as well as a representative Jupyter notebook to reproduce the main figures. Please
see the preprint on bioRxiv and the DOI link there to access the final published
version. Note the title change between the preprint and the published manuscript.\r\nA
sample script for particle-based simulations of collective chemotaxis by self-generated
gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb)
to generate exemplary cell trajectories. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt."
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960
apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023.
https://doi.org/10.5281/ZENODO.8133960.
ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and
a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.
ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.
mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo,
2023, doi:10.5281/ZENODO.8133960.
short: M.C. Ucar, (2023).
date_created: 2023-09-06T08:39:25Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-10-03T11:42:58Z
day: '11'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.8133960
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133960
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14274'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
file:
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file_size: 114932847
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date_created: 2023-10-04T10:11:21Z
date_updated: 2023-10-04T10:28:35Z
embargo: 2024-10-04
embargo_to: open_access
file_id: '14391'
file_name: PhD Thesis_Philipp Radler_20231004.pdf
file_size: 37838778
relation: main_file
file_date_updated: 2023-10-04T10:28:35Z
has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
month: '09'
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
- id: '10934'
relation: research_data
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Spatiotemporal signaling during assembly of the bacterial divisome
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '9034'
abstract:
- lang: eng
text: We determine an asymptotic formula for the number of integral points of bounded
height on a blow-up of P3 outside certain planes using universal torsors.
acknowledgement: This work was supported by the German Academic Exchange Service.
Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris
Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute
for its hospitality, as well as the anonymous referee for several useful remarks
and suggestions for improvements.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Florian Alexander
full_name: Wilsch, Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
citation:
ama: Wilsch FA. Integral points of bounded height on a log Fano threefold. International
Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048
apa: Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold.
International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048
chicago: Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log
Fano Threefold.” International Mathematics Research Notices. Oxford Academic,
2023. https://doi.org/10.1093/imrn/rnac048.
ieee: F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,”
International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic,
pp. 6780–6808, 2023.
ista: Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold.
International Mathematics Research Notices. 2023(8), 6780–6808.
mla: Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano
Threefold.” International Mathematics Research Notices, vol. 2023, no.
8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.
short: F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.
date_created: 2021-01-22T09:31:09Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-01T12:23:55Z
day: '01'
department:
- _id: TiBr
doi: 10.1093/imrn/rnac048
external_id:
arxiv:
- '1901.08503'
isi:
- '000773116000001'
intvolume: ' 2023'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.08503
month: '04'
oa: 1
oa_version: Preprint
page: 6780-6808
publication: International Mathematics Research Notices
publication_identifier:
eissn:
- 1687-0247
issn:
- 1073-7928
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
status: public
title: Integral points of bounded height on a log Fano threefold
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2023
year: '2023'
...
---
_id: '9651'
abstract:
- lang: eng
text: We introduce a hierachy of equivalence relations on the set of separated nets
of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞).
Two separated nets are called ϕ-displacement equivalent if, roughly speaking,
there is a bijection between them which, for large radii R, displaces points of
norm at most R by something of order at most ϕ(R). We show that the spectrum of
ϕ-displacement equivalence spans from the established notion of bounded displacement
equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation,
coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between
the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown
to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞.
We further undertake a comparison of our notion of ϕ-displacement equivalence
with previously studied relations on separated nets. Particular attention is given
to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz
equivalence.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). This work was started while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.
It was continued when the first named author was employed at University of Leipzig
and the second named author was employed at Institute of Science and Technology
of Austria, where he was supported by an IST Fellowship.'
article_number: '15'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Divergence of separated nets with respect to displacement
equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3
apa: Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect
to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3
chicago: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with
Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature,
2023. https://doi.org/10.1007/s10711-023-00862-3.
ieee: M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement
equivalence,” Geometriae Dedicata. Springer Nature, 2023.
ista: Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement
equivalence. Geometriae Dedicata., 15.
mla: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect
to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature,
2023, doi:10.1007/s10711-023-00862-3.
short: M. Dymond, V. Kaluza, Geometriae Dedicata (2023).
date_created: 2021-07-14T07:01:27Z
date_published: 2023-11-17T00:00:00Z
date_updated: 2024-01-11T13:06:32Z
day: '17'
department:
- _id: UlWa
doi: 10.1007/s10711-023-00862-3
external_id:
arxiv:
- '2102.13046'
isi:
- '001105681500001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10711-023-00862-3
month: '11'
oa: 1
oa_version: Published Version
publication: Geometriae Dedicata
publication_identifier:
eissn:
- 1572-9168
issn:
- 0046-5755
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence of separated nets with respect to displacement equivalence
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '9652'
abstract:
- lang: eng
text: In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated
nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice.
We study weaker notions of equivalence of separated nets and demonstrate that
such notions also give rise to distinct equivalence classes. Put differently,
we find occurrences of particularly strong divergence of separated nets from the
integer lattice. Our approach generalises that of Burago and Kleiner and McMullen
which takes place largely in a continuous setting. Existence of irregular separated
nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞).
In the present work we obtain stronger types of non-realisable densities.
acknowledgement: 'This work was done while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics.
2023;253:501-554. doi:10.1007/s11856-022-2448-6
apa: Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel
Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6
chicago: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.”
Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.
ieee: M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal
of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.
ista: Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal
of Mathematics. 253, 501–554.
mla: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel
Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.
short: M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.
date_created: 2021-07-14T07:01:28Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:26:34Z
day: '01'
ddc:
- '515'
- '516'
department:
- _id: UlWa
doi: 10.1007/s11856-022-2448-6
external_id:
arxiv:
- '1903.05923'
isi:
- '000904950300003'
file:
- access_level: open_access
checksum: 6fa0a3207dd1d6467c309fd1bcc867d1
content_type: application/pdf
creator: vkaluza
date_created: 2021-07-14T07:41:50Z
date_updated: 2021-07-14T07:41:50Z
file_id: '9653'
file_name: separated_nets.pdf
file_size: 900422
relation: main_file
file_date_updated: 2021-07-14T07:41:50Z
has_accepted_license: '1'
intvolume: ' 253'
isi: 1
keyword:
- Lipschitz
- bilipschitz
- bounded displacement
- modulus of continuity
- separated net
- non-realisable density
- Burago--Kleiner construction
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 501-554
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly irregular separated nets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 253
year: '2023'
...
---
_id: '10145'
abstract:
- lang: eng
text: We study direct integrals of quadratic and Dirichlet forms. We show that each
quasi-regular Dirichlet space over a probability space admits a unique representation
as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same
underlying topology. The same holds for each quasi-regular strongly local Dirichlet
space over a metrizable Luzin σ-finite Radon measure space, and admitting carré
du champ operator. In this case, the representation is only projectively unique.
acknowledgement: The author is grateful to Professors Sergio Albeverio and Andreas
Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the
present work, and for respectively pointing out the references [1, 13], and [3,
20]. Finally, he is especially grateful to an anonymous Reviewer for their very
careful reading and their suggestions which improved the readability of the paper.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
citation:
ama: Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals
and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y
apa: Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct
integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y
chicago: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct
Integrals and Applications.” Potential Analysis. Springer Nature, 2023.
https://doi.org/10.1007/s11118-021-09951-y.
ieee: L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals
and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615,
2023.
ista: Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct
integrals and applications. Potential Analysis. 58, 573–615.
mla: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct
Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature,
2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.
short: L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.
date_created: 2021-10-17T22:01:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-10-04T09:19:12Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s11118-021-09951-y
ec_funded: 1
external_id:
arxiv:
- '2003.01366'
isi:
- '000704213400001'
file:
- access_level: open_access
checksum: 625526482be300ca7281c91c30d41725
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:18:59Z
date_updated: 2023-10-04T09:18:59Z
file_id: '14387'
file_name: 2023_PotentialAnalysis_DelloSchiavo.pdf
file_size: 806391
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:18:59Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 573-615
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Potential Analysis
publication_identifier:
eissn:
- 1572-929X
issn:
- 0926-2601
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ergodic decomposition of Dirichlet forms via direct integrals and applications
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: 58
year: '2023'
...
---
_id: '10173'
abstract:
- lang: eng
text: We study the large scale behavior of elliptic systems with stationary random
coefficient that have only slowly decaying correlations. To this aim we analyze
the so-called corrector equation, a degenerate elliptic equation posed in the
probability space. In this contribution, we use a parabolic approach and optimally
quantify the time decay of the semigroup. For the theoretical point of view, we
prove an optimal decay estimate of the gradient and flux of the corrector when
spatially averaged over a scale R larger than 1. For the numerical point of view,
our results provide convenient tools for the analysis of various numerical methods.
acknowledgement: "I would like to thank my advisor Antoine Gloria for suggesting this
problem to me, as well for many interesting discussions and suggestions.\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Nicolas
full_name: Clozeau, Nicolas
id: fea1b376-906f-11eb-847d-b2c0cf46455b
last_name: Clozeau
citation:
ama: 'Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields. Stochastics and Partial Differential Equations:
Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w'
apa: 'Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic
homogenization for correlated coefficient fields. Stochastics and Partial
Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w'
chicago: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic
Homogenization for Correlated Coefficient Fields.” Stochastics and Partial
Differential Equations: Analysis and Computations. Springer Nature, 2023.
https://doi.org/10.1007/s40072-022-00254-w.'
ieee: 'N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields,” Stochastics and Partial Differential Equations:
Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.'
ista: 'Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization
for correlated coefficient fields. Stochastics and Partial Differential Equations:
Analysis and Computations. 11, 1254–1378.'
mla: 'Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic
Homogenization for Correlated Coefficient Fields.” Stochastics and Partial
Differential Equations: Analysis and Computations, vol. 11, Springer Nature,
2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.'
short: 'N. Clozeau, Stochastics and Partial Differential Equations: Analysis and
Computations 11 (2023) 1254–1378.'
date_created: 2021-10-23T10:50:22Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-14T11:51:47Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s40072-022-00254-w
external_id:
arxiv:
- '2102.07452'
isi:
- '000799715600001'
file:
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checksum: f83dcaecdbd3ace862c4ed97a20e8501
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:51:04Z
date_updated: 2023-08-14T11:51:04Z
file_id: '14052'
file_name: 2023_StochPartialDiffEquations_Clozeau.pdf
file_size: 1635193
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:51:04Z
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intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1254–1378
publication: 'Stochastics and Partial Differential Equations: Analysis and Computations'
publication_identifier:
issn:
- 2194-0401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal decay of the parabolic semigroup in stochastic homogenization for
correlated coefficient 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '10405'
abstract:
- lang: eng
text: 'We consider large non-Hermitian random matrices X with complex, independent,
identically distributed centred entries and show that the linear statistics of
their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives.
Previously this result was known only for a few special cases; either the test
functions were required to be analytic [72], or the distribution of the matrix
elements needed to be Gaussian [73], or at least match the Gaussian up to the
first four moments [82, 56]. We find the exact dependence of the limiting variance
on the fourth cumulant that was not known before. The proof relies on two novel
ingredients: (i) a local law for a product of two resolvents of the Hermitisation
of X with different spectral parameters and (ii) a coupling of several weakly
dependent Dyson Brownian motions. These methods are also the key inputs for our
analogous results on the linear eigenvalue statistics of real matrices X that
are presented in the companion paper [32]. '
acknowledgement: L.E. would like to thank Nathanaël Berestycki and D.S.would like
to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and
L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding
from the European Union’s Horizon 2020 research and in-novation programme under
the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max
Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue
statistics of non-Hermitian random matrices. Communications on Pure and Applied
Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem
for linear eigenvalue statistics of non-Hermitian random matrices. Communications
on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit
Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications
on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear
eigenvalue statistics of non-Hermitian random matrices,” Communications on
Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear
eigenvalue statistics of non-Hermitian random matrices. Communications on Pure
and Applied Mathematics. 76(5), 946–1034.
mla: Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics
of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics,
vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied
Mathematics 76 (2023) 946–1034.
date_created: 2021-12-05T23:01:41Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T09:22:55Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1002/cpa.22028
ec_funded: 1
external_id:
arxiv:
- '1912.04100'
isi:
- '000724652500001'
file:
- access_level: open_access
checksum: 8346bc2642afb4ccb7f38979f41df5d9
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:21:48Z
date_updated: 2023-10-04T09:21:48Z
file_id: '14388'
file_name: 2023_CommPureMathematics_Cipolloni.pdf
file_size: 803440
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:21:48Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 946-1034
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Communications on Pure and Applied Mathematics
publication_identifier:
eissn:
- 1097-0312
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Central limit theorem for linear eigenvalue statistics of non-Hermitian random
matrices
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: 76
year: '2023'
...
---
_id: '10550'
abstract:
- lang: eng
text: The global existence of renormalised solutions and convergence to equilibrium
for reaction-diffusion systems with non-linear diffusion are investigated. The
system is assumed to have quasi-positive non-linearities and to satisfy an entropy
inequality. The difficulties in establishing global renormalised solutions caused
by possibly degenerate diffusion are overcome by introducing a new class of weighted
truncation functions. By means of the obtained global renormalised solutions,
we study the large-time behaviour of complex balanced systems arising from chemical
reaction network theory with non-linear diffusion. When the reaction network does
not admit boundary equilibria, the complex balanced equilibrium is shown, by using
the entropy method, to exponentially attract all renormalised solutions in the
same compatibility class. This convergence extends even to a range of non-linear
diffusion, where global existence is an open problem, yet we are able to show
that solutions to approximate systems converge exponentially to equilibrium uniformly
in the regularisation parameter.
acknowledgement: "We thank the referees for their valuable comments and suggestions.
A major part of this work was carried out when B. Q. Tang visited the Institute
of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged.
This work was partially supported by NAWI Graz.\r\nOpen access funding provided
by University of Graz."
article_number: '66'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Klemens
full_name: Fellner, Klemens
last_name: Fellner
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
- first_name: Bao Quoc
full_name: Tang, Bao Quoc
last_name: Tang
citation:
ama: Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and
equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w
apa: Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion.
Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w
chicago: Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang.
“Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems
with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature,
2023. https://doi.org/10.1007/s00332-023-09926-w.
ieee: K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised
solutions and equilibration of reaction-diffusion systems with non-linear diffusion,”
Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.
ista: Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions
and equilibration of reaction-diffusion systems with non-linear diffusion. Journal
of Nonlinear Science. 33, 66.
mla: Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of
Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear
Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.
short: K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science
33 (2023).
date_created: 2021-12-16T12:15:35Z
date_published: 2023-06-07T00:00:00Z
date_updated: 2023-08-01T14:40:33Z
day: '07'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00332-023-09926-w
external_id:
arxiv:
- '2109.12019'
isi:
- '001002343400002'
file:
- access_level: open_access
checksum: f3f0f0886098e31c81116cff8183750b
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T07:33:53Z
date_updated: 2023-06-19T07:33:53Z
file_id: '13149'
file_name: 2023_JourNonlinearScience_Fellner.pdf
file_size: 742315
relation: main_file
success: 1
file_date_updated: 2023-06-19T07:33:53Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Journal of Nonlinear Science
publication_identifier:
eissn:
- 1432-1467
issn:
- 0938-8974
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global renormalised solutions and equilibration of reaction-diffusion systems
with non-linear diffusion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2023'
...
---
_id: '10551'
abstract:
- lang: eng
text: 'The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of
fluctuating hydrodynamics; it has been proposed in the physics literature to describe
the fluctuations of the density of N independent diffusing particles in the regime
of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation
presents a substantial challenge for both its analysis and its rigorous mathematical
justification. Besides being non-renormalisable by the theory of regularity structures
by Hairer et al., it has recently been shown to not even admit nontrivial martingale
solutions. In the present work, we give a rigorous and fully quantitative justification
of the Dean–Kawasaki equation by considering the natural regularisation provided
by standard numerical discretisations: We show that structure-preserving discretisations
of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting
diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In
other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate
and efficient numerical simulations of the density fluctuations of independent
diffusing particles.'
acknowledgement: "We thank the anonymous referee for his/her careful reading of the
manuscript and valuable suggestions. FC gratefully acknowledges funding from the
Austrian Science Fund (FWF) through the project F65, and from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science
Fund (FWF)."
article_number: '76'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density
fluctuations in systems of diffusing particles. Archive for Rational Mechanics
and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7
apa: Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the
structure of density fluctuations in systems of diffusing particles. Archive
for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7
chicago: Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and
the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive
for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7.
ieee: F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure
of density fluctuations in systems of diffusing particles,” Archive for Rational
Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023.
ista: Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure
of density fluctuations in systems of diffusing particles. Archive for Rational
Mechanics and Analysis. 247(5), 76.
mla: Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and
the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive
for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature,
2023, doi:10.1007/s00205-023-01903-7.
short: F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247
(2023).
date_created: 2021-12-16T12:16:03Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2024-01-30T12:10:10Z
day: '04'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00205-023-01903-7
ec_funded: 1
external_id:
arxiv:
- '2109.06500'
isi:
- '001043086800001'
file:
- access_level: open_access
checksum: 4529eeff170b6745a461d397ee611b5a
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:09:34Z
date_updated: 2024-01-30T12:09:34Z
file_id: '14904'
file_name: 2023_ArchiveRationalMech_Cornalba.pdf
file_size: 1851185
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:09:34Z
has_accepted_license: '1'
intvolume: ' 247'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Dean-Kawasaki equation and the structure of density fluctuations in systems
of diffusing particles
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: 247
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
arxiv: 1
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: '12086'
abstract:
- lang: eng
text: We present a simple algorithm for computing higher-order Delaunay mosaics
that works in Euclidean spaces of any finite dimensions. The algorithm selects
the vertices of the order-k mosaic from incrementally constructed lower-order
mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box
to construct the order-k mosaic from its vertices. Beyond this black-box, the
algorithm uses only combinatorial operations, thus facilitating easy implementation.
We extend this algorithm to compute higher-order α-shapes and provide open-source
implementations. We present experimental results for properties of higher-order
Delaunay mosaics of random point sets.
acknowledgement: Open access funding provided by Austrian Science Fund (FWF). This
project has received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme, 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.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
citation:
ama: Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics
and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6
apa: Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order
Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6
chicago: Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order
Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023.
https://doi.org/10.1007/s00453-022-01027-6.
ieee: H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay
mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp.
277–295, 2023.
ista: Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay
mosaics and alpha shapes. Algorithmica. 85, 277–295.
mla: Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order
Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature,
2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.
short: H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.
date_created: 2022-09-11T22:01:57Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-06-27T12:53:43Z
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ddc:
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doi: 10.1007/s00453-022-01027-6
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call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
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name: The Wittgenstein Prize
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call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Algorithmica
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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title: A simple algorithm for higher-order Delaunay mosaics and alpha shapes
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abstract:
- lang: eng
text: Following up on the recent work on lower Ricci curvature bounds for quantum
systems, we introduce two noncommutative versions of curvature-dimension bounds
for symmetric quantum Markov semigroups over matrix algebras. Under suitable such
curvature-dimension conditions, we prove a family of dimension-dependent functional
inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power
in the noncommutative setting. We also provide examples satisfying certain curvature-dimension
conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers
over group algebras and generalized depolarizing semigroups.
acknowledgement: H.Z. is supported by the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411
and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges
support from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (Grant Agreement No. 716117) and from the
Austrian Science Fund (FWF) through grant number F65. Both authors would like to
thank Jan Maas for fruitful discussions and helpful comments. Open access funding
provided by Austrian Science Fund (FWF).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov
semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x
apa: Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric
quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x
chicago: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for
Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer
Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x.
ieee: M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum
Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp.
717–750, 2023.
ista: Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum
Markov semigroups. Annales Henri Poincare. 24, 717–750.
mla: Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric
Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.
short: M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.
date_created: 2022-09-11T22:01:57Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:39:28Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00023-022-01220-x
ec_funded: 1
external_id:
arxiv:
- '2105.08303'
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- '000837499800002'
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language:
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month: '03'
oa: 1
oa_version: Published Version
page: 717-750
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
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grant_number: F6504
name: Taming Complexity in Partial Differential 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: Curvature-dimension conditions for symmetric quantum Markov semigroups
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...