---
OA_place: publisher
_id: '18979'
abstract:
- lang: eng
text: "Topological Data Analysis (TDA) is a discipline utilizing the mathematical
field of topology to study data, most prominently collections of point sets. This
thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first
one establishes a variant of TDA for chromatic point sets, where each point is
given a color. For example, we are given positions of cells within a tumor microenvironment,
and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is
then to give a quantitative description of how the two or more sets of points
spatially interact. Building on image, kernel and cokernel variants of persistent
homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe
describe a construction of a chromatic alpha complex, which enables efficient
computation of several variants of the six-packs. We give topological descriptions
of natural subcomplexes of the chromatic alpha complex, and show that the radii
of the simplices form a discrete Morse function. Finally, we provide an implementation
of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate
a powerful tool of sheaf theory to elementary terms using labeled matrices. The
goal is to enable their use in computational settings. We show that derived categories
of sheaves over finite posets have, up to isomorphism, unique objects---minimal
injective resolutions---and give a concrete algorithm to compute them. We further
describe simple algorithms to compute derived pushforwards and pullbacks for monotonic
maps, and their proper variants for inclusions, and demonstrate their tractability
by providing an implementation. Finally, we suggest a discrete definition of microsupport
and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the
last part, we present a collection of observations about collapses. We give a
characterization of collapsibility in terms of unitriangular submatrices of the
boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant
of the Procrustes problem. We establish relation between dual collapses and relative
Morse theory and pose several open questions. Finally, focusing on complexes embedded
in the three-dimensional Euclidean space, we describe a relation between the collapsibility
and the triviality of a polygonal knot."
acknowledgement: "The research presented in this thesis was funded with the Wittgenstein
Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative
Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian
Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ondrej
full_name: Draganov, Ondrej
id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
last_name: Draganov
orcid: 0000-0003-0464-3823
citation:
ama: Draganov O. Structures and computations in topological data analysis. 2025.
doi:10.15479/at:ista:18979
apa: Draganov, O. (2025). Structures and computations in topological data analysis.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18979
chicago: Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18979.
ieee: O. Draganov, “Structures and computations in topological data analysis,” Institute
of Science and Technology Austria, 2025.
ista: Draganov O. 2025. Structures and computations in topological data analysis.
Institute of Science and Technology Austria.
mla: Draganov, Ondrej. Structures and Computations in Topological Data Analysis.
Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18979.
short: O. Draganov, Structures and Computations in Topological Data Analysis, Institute
of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-01-31T17:04:40Z
date_published: 2025-02-03T00:00:00Z
date_updated: 2026-04-07T11:47:30Z
day: '03'
ddc:
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- '004'
degree_awarded: PhD
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- _id: HeEd
doi: 10.15479/at:ista:18979
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file_date_updated: 2025-02-04T16:22:07Z
fulldoi: https://doi.org/10.15479/at:ista:18979
has_accepted_license: '1'
keyword:
- topological data analysis
- chromatic point set
- alpha complex
- persistent homology
- six pack
- sheaf
- microlocal discrete Morse
- injective resolution
- collapse
- knot
- discrete Morse theory
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '140'
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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status: public
- id: '18981'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Structures and computations in topological data analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: gold
_id: '18991'
abstract:
- lang: eng
text: Research data for the article "Learning reshapes the hippocampal representation
hierarchy" from Chiossi et al. (PNAS, 2025). The data includes hippocampal CA1
unit activity and behaviour tracking of 5 Long Evans rats during the learning
of an associative memory task. Detailed information can be found in the 'readme.txt'
file.
acknowledged_ssus:
- _id: PreCl
- _id: M-Shop
acknowledgement: Thanks to Rebecca Morse for performing one of the experiments under
H.S.C.C. supervision and Jago Wallenschus for technical support, especially with
maze design.
article_processing_charge: No
author:
- first_name: Heloisa
full_name: Chiossi, Heloisa
id: 2BBA502C-F248-11E8-B48F-1D18A9856A87
last_name: Chiossi
orcid: 0009-0004-2973-278X
citation:
ama: Chiossi HSC. Research data for the publication “Learning reshapes the hippocampal
representation hierarchy.” 2025. doi:10.15479/AT:ISTA:18991
apa: Chiossi, H. S. C. (2025). Research data for the publication “Learning reshapes
the hippocampal representation hierarchy.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:18991
chicago: Chiossi, Heloisa S. C. “Research Data for the Publication ‘Learning Reshapes
the Hippocampal Representation Hierarchy.’” Institute of Science and Technology
Austria, 2025. https://doi.org/10.15479/AT:ISTA:18991.
ieee: H. S. C. Chiossi, “Research data for the publication ‘Learning reshapes the
hippocampal representation hierarchy.’” Institute of Science and Technology Austria,
2025.
ista: Chiossi HSC. 2025. Research data for the publication ‘Learning reshapes the
hippocampal representation hierarchy’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:18991.
mla: Chiossi, Heloisa S. C. Research Data for the Publication “Learning Reshapes
the Hippocampal Representation Hierarchy.” Institute of Science and Technology
Austria, 2025, doi:10.15479/AT:ISTA:18991.
short: H.S.C. Chiossi, (2025).
contributor:
- contributor_type: researcher
first_name: Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- contributor_type: supervisor
first_name: Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
corr_author: '1'
date_created: 2025-02-04T10:36:18Z
date_published: 2025-02-04T00:00:00Z
date_updated: 2026-05-06T13:12:00Z
day: '04'
ddc:
- '570'
department:
- _id: GradSch
- _id: JoCs
- _id: GaTk
doi: 10.15479/AT:ISTA:18991
file:
- access_level: open_access
checksum: 04d761ed42e8879abffde04a560409ce
content_type: application/zip
creator: hchiossi
date_created: 2025-02-04T10:16:52Z
date_updated: 2025-02-04T10:16:52Z
file_id: '18992'
file_name: Chiossi_etal_2025_PNAS_data.zip
file_size: 769383201
relation: main_file
success: 1
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checksum: 50602931dcd33e4f009ed46af11335f3
content_type: text/plain
creator: hchiossi
date_created: 2025-02-04T10:18:33Z
date_updated: 2025-02-04T10:18:33Z
file_id: '18993'
file_name: readme.txt
file_size: 3215
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success: 1
file_date_updated: 2025-02-04T10:18:33Z
fulldoi: https://doi.org/10.15479/AT:ISTA:18991
has_accepted_license: '1'
keyword:
- hippocampus
- electrophysiology
- behavior
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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status: public
title: Research data for the publication "Learning reshapes the hippocampal representation
hierarchy"
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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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '19048'
abstract:
- lang: eng
text: 'Rotations are found in physics problems at all scales: from spatial motion
of celestial bodies, to transitions between quantum states of atoms and molecules.
Mathematically, they represent a fundamental class of transformations and symmetries.
Unlike spatial displacements, rotational transformations in three-dimensional
space are non-commutative: the result of applying a sequence of rotations depends
on the order of these operations. This feature makes the emergent physics that
involves rotations rather intricate, but instrumental for studies of highly-interconnected
many-body systems. In the presence of an environment, rotational properties of
an object change, due to the interaction with particles of the environment. Owing
to the complexity of this interaction, it can be engineered to exhibit certain
properties of interest. In this Thesis, we examine several scenarios of how the
rotational behavior of an impurity can be modified by interactions with its environment.'
acknowledged_ssus:
- _id: CampIT
- _id: E-Lib
- _id: SSU
acknowledgement: "I am grateful to the European Research Council (ERC) [10.3030/801770]
and Austrian\r\nScience Fund (FWF) [10.55776/F1004] for funding my research and
to the Physical\r\nReview journals for publishing it. I also want to thank the VCQ
(previously CoQuS) and\r\nIQOQI for organizing wonderful networking events for the
physics community in Vienna\r\nand Innsbruck, respectively. Moreover, I thank Austrian
Science Fund (FWF) for the\r\ncontinuous support for quantum research."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
citation:
ama: Maslov M. Emergent physics of rotating quantum impurities in many-body environments.
2025. doi:10.15479/at:ista:19048
apa: Maslov, M. (2025). Emergent physics of rotating quantum impurities in many-body
environments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:19048
chicago: Maslov, Mikhail. “Emergent Physics of Rotating Quantum Impurities in Many-Body
Environments.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:19048.
ieee: M. Maslov, “Emergent physics of rotating quantum impurities in many-body environments,”
Institute of Science and Technology Austria, 2025.
ista: Maslov M. 2025. Emergent physics of rotating quantum impurities in many-body
environments. Institute of Science and Technology Austria.
mla: Maslov, Mikhail. Emergent Physics of Rotating Quantum Impurities in Many-Body
Environments. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:19048.
short: M. Maslov, Emergent Physics of Rotating Quantum Impurities in Many-Body Environments,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-02-18T01:41:27Z
date_published: 2025-02-18T00:00:00Z
date_updated: 2026-04-16T12:20:38Z
day: '18'
ddc:
- '539'
- '535'
- '541'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiLe
doi: 10.15479/at:ista:19048
ec_funded: 1
file:
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creator: mmaslov
date_created: 2025-02-18T14:25:59Z
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file_size: 14453726
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has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '86'
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3
grant_number: F100403
name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10845'
relation: part_of_dissertation
status: public
- id: '7933'
relation: part_of_dissertation
status: public
- id: '18087'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Emergent physics of rotating quantum impurities in many-body environments
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19066'
abstract:
- lang: eng
text: "We present a sample of 1956 individual stellar clumps at redshift 0.7 < z
< 10, detected with JWST/NIRCam in 476 galaxies lensed by the galaxy cluster Abell2744.
The lensed clumps present magnifications ranging between μ = 1.8 and μ = 300.
We perform simultaneous size-photometry estimates in 20 JWST/NIRCam median and
broad-band filters from 0.7 to 5 μm.\r\nSpectral energy distribution (SED) fitting
analyses enable us to recover the physical properties of the clumps. The majority
of the clumps are spatially resolved and have effective radii in the range Reff
= 10–700 pc. We restrict this first study to the 1751 post-reionization era clumps
with redshift < 5.5. We find a significant evolution of the average clump ages,
star formation rates (SFRs), SFR surface densities, and metallicity with increasing
redshift, while median stellar mass and stellar mass surface densities are similar
in the probed redshift range. We observe a strong correlation between the clump
properties and the properties of their host galaxies, with more massive galaxies
hosting more massive and older clumps. We find that clumps closer to their host
galactic centre are on average more massive, while their ages do not show clear
sign of migration. We find that clumps at cosmic noon sample the upper-mass end
of the mass function to higher masses than at z > 3, reflecting the rapid increase
towards the peak of the cosmic star formation history. We conclude that the results
achieved over the studied redshift range are in agreement with expectation of
in situ clump formation scenario from large-scale disc fragmentation. "
acknowledgement: 'The authors thank the International Space Science Institute for
sponsoring the ISSI team: ‘Star Formation within rapidly evolving galaxies’ where
many ideas discussed in this article have been brainstormed. AA and AC acknowledge
support by the Swedish research council Vetenskapsrådet (2021-05559). MM acknowledges
the financial support through grant PRIN-MIUR 2020SKSTHZ. JM and IK acknowledge
support by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed
are however those of the author(s) only and do not necessarily reflect those of
the European Union or the European Research Council. Neither the European Union
nor the granting authority can be held responsible for them. RPN acknowledges funding
from JWST programme GO-3516. Support for this work was provided by NASA through
the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope
Science Institute, which is operated by the Association of Universities for Research
in Astronomy, Incorporated, under NASA contract NAS5-26555.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Adélaïde
full_name: Claeyssens, Adélaïde
last_name: Claeyssens
- first_name: Angela
full_name: Adamo, Angela
last_name: Adamo
- first_name: Matteo
full_name: Messa, Matteo
last_name: Messa
- first_name: Miroslava
full_name: Dessauges-Zavadsky, Miroslava
last_name: Dessauges-Zavadsky
- first_name: Johan
full_name: Richard, Johan
last_name: Richard
- first_name: Ivan
full_name: Kramarenko, Ivan
id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4
last_name: Kramarenko
orcid: 0000-0001-5346-6048
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
citation:
ama: Claeyssens A, Adamo A, Messa M, et al. Tracing star formation across cosmic
time at tens of parsec-scales in the lensing cluster field Abell 2744. Monthly
Notices of the Royal Astronomical Society. 2025;537(3):2535-2558. doi:10.1093/mnras/staf058
apa: Claeyssens, A., Adamo, A., Messa, M., Dessauges-Zavadsky, M., Richard, J.,
Kramarenko, I., … Naidu, R. P. (2025). Tracing star formation across cosmic time
at tens of parsec-scales in the lensing cluster field Abell 2744. Monthly Notices
of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staf058
chicago: Claeyssens, Adélaïde, Angela Adamo, Matteo Messa, Miroslava Dessauges-Zavadsky,
Johan Richard, Ivan Kramarenko, Jorryt J Matthee, and Rohan P. Naidu. “Tracing
Star Formation across Cosmic Time at Tens of Parsec-Scales in the Lensing Cluster
Field Abell 2744.” Monthly Notices of the Royal Astronomical Society. Oxford
University Press, 2025. https://doi.org/10.1093/mnras/staf058.
ieee: A. Claeyssens et al., “Tracing star formation across cosmic time at
tens of parsec-scales in the lensing cluster field Abell 2744,” Monthly Notices
of the Royal Astronomical Society, vol. 537, no. 3. Oxford University Press,
pp. 2535–2558, 2025.
ista: Claeyssens A, Adamo A, Messa M, Dessauges-Zavadsky M, Richard J, Kramarenko
I, Matthee JJ, Naidu RP. 2025. Tracing star formation across cosmic time at tens
of parsec-scales in the lensing cluster field Abell 2744. Monthly Notices of the
Royal Astronomical Society. 537(3), 2535–2558.
mla: Claeyssens, Adélaïde, et al. “Tracing Star Formation across Cosmic Time at
Tens of Parsec-Scales in the Lensing Cluster Field Abell 2744.” Monthly Notices
of the Royal Astronomical Society, vol. 537, no. 3, Oxford University Press,
2025, pp. 2535–58, doi:10.1093/mnras/staf058.
short: A. Claeyssens, A. Adamo, M. Messa, M. Dessauges-Zavadsky, J. Richard, I.
Kramarenko, J.J. Matthee, R.P. Naidu, Monthly Notices of the Royal Astronomical
Society 537 (2025) 2535–2558.
date_created: 2025-02-23T23:01:55Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2026-02-16T11:51:48Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
- _id: GradSch
doi: 10.1093/mnras/staf058
external_id:
arxiv:
- '2410.10974'
isi:
- '001420026000001'
file:
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checksum: 431aef05755e6b5472f5e9b4c326cf84
content_type: application/pdf
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date_updated: 2025-02-25T06:38:43Z
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file_size: 35099276
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file_date_updated: 2025-02-25T06:38:43Z
fulldoi: https://doi.org/10.1093/mnras/staf058
has_accepted_license: '1'
intvolume: ' 537'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 2535-2558
project:
- _id: bd9b2118-d553-11ed-ba76-db24564edfea
grant_number: '101076224'
name: Young galaxies as tracers and agents of cosmic reionization
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing star formation across cosmic time at tens of parsec-scales in the lensing
cluster field Abell 2744
tmp:
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 537
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19067'
abstract:
- lang: eng
text: Modern experimental methods enable the creation of self-assembly building
blocks with tunable interactions, but optimally exploiting this tunability for
the self-assembly of desired structures remains an important challenge. Many studies
of this inverse problem start with the so-called fully addressable limit, where
every particle in a target structure is different. This leads to clear design
principles that often result in high assembly yield, but it is not a scalable
approach—at some point, one must grapple with “reusing” building blocks, which
lowers the degree of addressability and may cause a multitude of off-target structures
to form, complicating the design process. Here, we solve a key obstacle preventing
robust inverse design in the “semiaddressable regime” by developing a highly efficient
algorithm that enumerates all structures that can be formed from a given set of
building blocks. By combining this with established partition-function-based yield
calculations, we show that it is almost always possible to find economical semiaddressable
designs where the entropic gain from reusing building blocks outweighs the presence
of off-target structures and even increases the yield of the target. Thus, not
only does our enumeration algorithm enable robust and scalable inverse design
in the semiaddressable regime, our results demonstrate that it is possible to
operate in this regime while maintaining the level of control often associated
with full addressability.
acknowledgement: We thank Daichi Hayakawa, Thomas E. Videbæk, and W. Benjamin Rogers
for important discussions and Jérémie Palacci, Anđela Šarić, and Scott Waitukaitis
for helpful comments on the manuscript. The research was supported by the Gesellschaft
für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.
article_number: '058204'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: Hübl M, Goodrich CP. Accessing semiaddressable self-assembly with efficient
structure enumeration. Physical Review Letters. 2025;134(5). doi:10.1103/PhysRevLett.134.058204
apa: Hübl, M., & Goodrich, C. P. (2025). Accessing semiaddressable self-assembly
with efficient structure enumeration. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.134.058204
chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly
with Efficient Structure Enumeration.” Physical Review Letters. American
Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.058204.
ieee: M. Hübl and C. P. Goodrich, “Accessing semiaddressable self-assembly with
efficient structure enumeration,” Physical Review Letters, vol. 134, no.
5. American Physical Society, 2025.
ista: Hübl M, Goodrich CP. 2025. Accessing semiaddressable self-assembly with efficient
structure enumeration. Physical Review Letters. 134(5), 058204.
mla: Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly
with Efficient Structure Enumeration.” Physical Review Letters, vol. 134,
no. 5, 058204, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.058204.
short: M. Hübl, C.P. Goodrich, Physical Review Letters 134 (2025).
corr_author: '1'
date_created: 2025-02-23T23:01:55Z
date_published: 2025-02-07T00:00:00Z
date_updated: 2025-09-30T10:35:47Z
day: '07'
department:
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doi: 10.1103/PhysRevLett.134.058204
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pmid: 1
project:
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grant_number: FTI23-G-011
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publication: Physical Review Letters
publication_identifier:
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abstract:
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text: "This .zip file contains the data to reproduce the figures and supplementary
figures of \"Exchange anisotropies in microwave-driven singlet-triplet qubits\"
by Jaime Saez-Mollejo et al.\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "We thank A. Crippa for helpful discussions. This research was supported
by the Scientific Service Units of ISTA through resources provided by the MIBA Machine
Shop and the Nanofabrication facility. This research and related results were made
possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project
and the FWF Projects \r\nwith DOI:10.55776/F86 and DOI:10.55776/I5060. M.R.-R. acknowledges
support from the Netherlands Organization of\r\n scientific Research (NWO) under
Veni grant VI.Veni.212.223. The Research of S.B. and M.R.-R. was sponsored in part
by the Army Research Office and was accomplished under Award Number: W911NF-23-1-0110."
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citation:
ama: Saez Mollejo J. Exchange anisotropies in microwave-driven singlet-triplet qubits.
2025. doi:10.15479/AT:ISTA:19409
apa: Saez Mollejo, J. (2025). Exchange anisotropies in microwave-driven singlet-triplet
qubits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:19409
chicago: Saez Mollejo, Jaime. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet
Qubits.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:19409.
ieee: J. Saez Mollejo, “Exchange anisotropies in microwave-driven singlet-triplet
qubits.” Institute of Science and Technology Austria, 2025.
ista: Saez Mollejo J. 2025. Exchange anisotropies in microwave-driven singlet-triplet
qubits, Institute of Science and Technology Austria, 10.15479/AT:ISTA:19409.
mla: Saez Mollejo, Jaime. Exchange Anisotropies in Microwave-Driven Singlet-Triplet
Qubits. Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:19409.
short: J. Saez Mollejo, (2025).
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last_name: Rimbach-Russ
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last_name: Bosco
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id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
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abstract:
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text: In standard quantum electrodynamics (QED), the so-called non-minimal (Pauli)
coupling is suppressed for elementary particles and has no physical implications.
Here, we show that the Pauli term naturally appears in a known family of Dirac
materials—the lead-halide perovskites, suggesting a novel playground for the study
of analog QED effects. We outline measurable manifestations of the Pauli term
in the phenomena pertaining to (i) relativistic corrections to bound states (ii)
the Klein paradox, and (iii) spin effects in scattering. In particular, we demonstrate
that (a) the binding energy of an electron in the vicinity of a positively charged
defect is noticeably decreased due to the polarizability of lead ions and the
appearance of a Darwin-like term, (b) strong spin-orbit coupling due to the Pauli
term affects the exciton states, and (c) scattering of an electron off an energy
barrier with broken mirror symmetry produces spin polarization in the outgoing
current. Our study adds to the understanding of quantum phenomena in lead-halide
perovskites and paves the way for tabletop simulations of analog Dirac-Pauli equations.
article_number: '37'
article_processing_charge: Yes
article_type: original
author:
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Shiva Kumar A, Maslov M, Lemeshko M, Volosniev A, Alpichshev Z. Massive Dirac-Pauli
physics in lead-halide perovskites. npj Quantum Materials. 2025;10. doi:10.1038/s41535-025-00754-7
apa: Shiva Kumar, A., Maslov, M., Lemeshko, M., Volosniev, A., & Alpichshev,
Z. (2025). Massive Dirac-Pauli physics in lead-halide perovskites. Npj Quantum
Materials. Springer Nature. https://doi.org/10.1038/s41535-025-00754-7
chicago: Shiva Kumar, Abhishek, Mikhail Maslov, Mikhail Lemeshko, Artem Volosniev,
and Zhanybek Alpichshev. “Massive Dirac-Pauli Physics in Lead-Halide Perovskites.”
Npj Quantum Materials. Springer Nature, 2025. https://doi.org/10.1038/s41535-025-00754-7.
ieee: A. Shiva Kumar, M. Maslov, M. Lemeshko, A. Volosniev, and Z. Alpichshev, “Massive
Dirac-Pauli physics in lead-halide perovskites,” npj Quantum Materials,
vol. 10. Springer Nature, 2025.
ista: Shiva Kumar A, Maslov M, Lemeshko M, Volosniev A, Alpichshev Z. 2025. Massive
Dirac-Pauli physics in lead-halide perovskites. npj Quantum Materials. 10, 37.
mla: Shiva Kumar, Abhishek, et al. “Massive Dirac-Pauli Physics in Lead-Halide Perovskites.”
Npj Quantum Materials, vol. 10, 37, Springer Nature, 2025, doi:10.1038/s41535-025-00754-7.
short: A. Shiva Kumar, M. Maslov, M. Lemeshko, A. Volosniev, Z. Alpichshev, Npj
Quantum Materials 10 (2025).
corr_author: '1'
date_created: 2025-04-08T18:13:06Z
date_published: 2025-04-04T00:00:00Z
date_updated: 2026-05-06T13:06:08Z
day: '04'
ddc:
- '530'
department:
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- _id: ZhAl
- _id: MiLe
doi: 10.1038/s41535-025-00754-7
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publication: npj Quantum Materials
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title: Massive Dirac-Pauli physics in lead-halide perovskites
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acknowledged_ssus:
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acknowledgement: "The work presented in this doctoral thesis was performed at the
Institute of Science\r\nand Technology (ISTA) and financially supported by a European
Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02)
and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very
thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering
me financial\r\nsupport to perform essential experiments during my PhD studies and
to participate in\r\ninternational conferences and courses."
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models at single-cell resolution. 2025. doi:10.15479/AT-ISTA-19557
apa: Schwarz, L. A. (2025). Mapping developmental dynamics of autism spectrum
disorder mouse models at single-cell resolution. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-19557
chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19557.
ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder
mouse models at single-cell resolution,” Institute of Science and Technology Austria,
2025.
ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder
mouse models at single-cell resolution. Institute of Science and Technology Austria.
mla: Schwarz, Lena A. Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution. Institute of Science and Technology
Austria, 2025, doi:10.15479/AT-ISTA-19557.
short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria,
2025.
corr_author: '1'
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supervisor:
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id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Mapping developmental dynamics of autism spectrum disorder mouse models at
single-cell resolution
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...
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abstract:
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text: In this article, we propose a method for generating single microwave photons
in superconducting circuits. We theoretically show that pure single microwave
photons can be generated on demand and tuned over a large frequency band by making
use of Landau-Zener transitions under a rapid sweep of a control parameter. We
devise a protocol that enables fast control of the frequency of the emitted photon
over two octaves, without requiring extensive calibration. Additionally, we make
theoretical estimates of the generation efficiency, tunability, purity, and linewidth
of the photons emitted using this method for both charge- and flux-qubit-based
architectures. We also provide estimates of the optimal device parameters required
for these architectures to realize the device.
acknowledgement: The authors acknowledge the support of DST-INSPIRE Fellowship No.
IF180339 and DST-SERB Core Research Grant No. CRG/2018/002129. S.H. acknowledges
the support of the Kishore Vaigyanik Protsahan Yojana (KVPY). S.H. also acknowledges
helpful discussions with Harsh Arora and Johannes Fink.
article_number: '044042'
article_processing_charge: Yes (via OA deal)
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author:
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full_name: Hawaldar, Samarth
id: 221708e1-1ff6-11ee-9fa6-85146607433e
last_name: Hawaldar
orcid: 0000-0002-1965-4309
- first_name: Siddhi Satish
full_name: Khaire, Siddhi Satish
last_name: Khaire
- first_name: Per
full_name: Delsing, Per
last_name: Delsing
- first_name: Baladitya
full_name: Suri, Baladitya
last_name: Suri
citation:
ama: Hawaldar S, Khaire SS, Delsing P, Suri B. On-demand single-microwave-photon
source in a superconducting circuit with wideband frequency tunability. Physical
Review Applied. 2025;23(4). doi:10.1103/physrevapplied.23.044042
apa: Hawaldar, S., Khaire, S. S., Delsing, P., & Suri, B. (2025). On-demand
single-microwave-photon source in a superconducting circuit with wideband frequency
tunability. Physical Review Applied. American Physical Society. https://doi.org/10.1103/physrevapplied.23.044042
chicago: Hawaldar, Samarth, Siddhi Satish Khaire, Per Delsing, and Baladitya Suri.
“On-Demand Single-Microwave-Photon Source in a Superconducting Circuit with Wideband
Frequency Tunability.” Physical Review Applied. American Physical Society,
2025. https://doi.org/10.1103/physrevapplied.23.044042.
ieee: S. Hawaldar, S. S. Khaire, P. Delsing, and B. Suri, “On-demand single-microwave-photon
source in a superconducting circuit with wideband frequency tunability,” Physical
Review Applied, vol. 23, no. 4. American Physical Society, 2025.
ista: Hawaldar S, Khaire SS, Delsing P, Suri B. 2025. On-demand single-microwave-photon
source in a superconducting circuit with wideband frequency tunability. Physical
Review Applied. 23(4), 044042.
mla: Hawaldar, Samarth, et al. “On-Demand Single-Microwave-Photon Source in a Superconducting
Circuit with Wideband Frequency Tunability.” Physical Review Applied, vol.
23, no. 4, 044042, American Physical Society, 2025, doi:10.1103/physrevapplied.23.044042.
short: S. Hawaldar, S.S. Khaire, P. Delsing, B. Suri, Physical Review Applied 23
(2025).
corr_author: '1'
date_created: 2025-04-24T06:34:07Z
date_published: 2025-04-18T00:00:00Z
date_updated: 2025-09-30T12:17:33Z
day: '18'
ddc:
- '539'
department:
- _id: GradSch
- _id: JoFi
doi: 10.1103/physrevapplied.23.044042
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issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review Applied
publication_identifier:
issn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On-demand single-microwave-photon source in a superconducting circuit with
wideband frequency tunability
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19621'
abstract:
- lang: eng
text: In this paper we obtain a complete description of all indecomposable characters
(central positive-definite functions) of inductive limits of the symmetric groups
under block diagonal embedding. As a corollary we obtain the full classification
of the isomorphism classes of these inductive limits.
acknowledgement: The authors were partially supported by the “Long-term program of
support of the Ukrainian research teams at the Polish Academy of Sciences carried
out in collaboration with the U.S. National Academy of Sciences with the financial
support of external partners”. The second author was also supported by the Austrian
Science Fund (FWF) grant “Geometry of the tip of the global nilpotent cone” no.
10.55776/P35847
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Nikolay
full_name: Nessonov, Nikolay
last_name: Nessonov
- first_name: Nhok T
full_name: Ngo, Nhok T
id: 28e53c8c-896a-11ed-bdf8-f809043ce2f0
last_name: Ngo
citation:
ama: Nessonov N, Ngo NT. Indecomposable characters of inductive limits of symmetric
groups. Representation Theory. 2025;29(8):256-288. doi:10.1090/ert/689
apa: Nessonov, N., & Ngo, N. T. (2025). Indecomposable characters of inductive
limits of symmetric groups. Representation Theory. American Mathematical
Society. https://doi.org/10.1090/ert/689
chicago: Nessonov, Nikolay, and Nhok T Ngo. “Indecomposable Characters of Inductive
Limits of Symmetric Groups.” Representation Theory. American Mathematical
Society, 2025. https://doi.org/10.1090/ert/689.
ieee: N. Nessonov and N. T. Ngo, “Indecomposable characters of inductive limits
of symmetric groups,” Representation Theory, vol. 29, no. 8. American Mathematical
Society, pp. 256–288, 2025.
ista: Nessonov N, Ngo NT. 2025. Indecomposable characters of inductive limits of
symmetric groups. Representation Theory. 29(8), 256–288.
mla: Nessonov, Nikolay, and Nhok T. Ngo. “Indecomposable Characters of Inductive
Limits of Symmetric Groups.” Representation Theory, vol. 29, no. 8, American
Mathematical Society, 2025, pp. 256–88, doi:10.1090/ert/689.
short: N. Nessonov, N.T. Ngo, Representation Theory 29 (2025) 256–288.
corr_author: '1'
date_created: 2025-04-24T08:48:05Z
date_published: 2025-04-10T00:00:00Z
date_updated: 2025-05-05T06:59:07Z
day: '10'
ddc:
- '510'
department:
- _id: GradSch
- _id: TaHa
doi: 10.1090/ert/689
external_id:
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- '2206.01964'
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success: 1
file_date_updated: 2025-05-05T06:57:49Z
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intvolume: ' 29'
issue: '8'
language:
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license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
page: 256-288
project:
- _id: 34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3
grant_number: P35847
name: Geometry of the tip of the global nilpotent cone
publication: Representation Theory
publication_identifier:
issn:
- 1088-4165
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Indecomposable characters of inductive limits of symmetric groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2025'
...
---
OA_place: publisher
_id: '19630'
abstract:
- lang: eng
text: "This thesis consists of three chapters, each corresponding to one publication.
While each of these projects tackles a topic in a different area of research,
they all share a common thread in the type of topological structure they handle
- a partition of space into volumes separated by interfaces that meet in non-manifold
junctions.\r\n\r\nIn Chapter 2, we study clusters of soap bubbles from a simulation
perspective. In particular, we develop a surface-only algorithm that couples large
scale motion and shape deformation of soap bubble clusters with the small scale
evolution of the thin film's thickness, which is responsible for visual phenomena
like surface vortices, Newton's interference patterns, capillary waves, and deformation-dependent
rupturing of films in a foam. We model film thickness as a reduced degree of freedom
in the Navier-Stokes equations and from them derive three sets of equations governing
normal and tangential motion of the soap film surface, as well as the evolution
of the thin film thickness. We discretize these equations on a non-manifold triangle
mesh, extending and adapting operators to handle complex topology. We also present
an incompressible fluid solver for 2.5D films and an advection algorithm for convecting
fields across non-manifold surface junctions. Our simulations enhance bubble solvers
with additional effects caused by convection, rippling, draining, and evaporation
of the thin film.\r\n\r\nIn Chapter 3, we introduce a multi-material non-manifold
mesh-based surface tracking algorithm that converts mesh defects, such as overlaps,
self-intersections, and inversions into topological changes. Our algorithm generalizes
prior work on manifold surface tracking with topological changes: it preserves
surface features like mesh-based methods, and it robustly handles topological
changes like level set methods. Our method also offers improved efficiency and
robustness over the state of the art. We demonstrate the effectiveness of the
approach on a range of examples, including complex soap film simulations, such
as those presented in Chapter 2, but with an order of magnitude more interacting
bubbles than what we could achieve before, and Boolean unions of non-manifold
meshes consisting of millions of triangles.\r\n\r\nLastly, in Chapter 4, we utilize
developments in the theory of random geometric complexes facilitated by observations
from Discrete Morse theory. We survey the methods and results obtained with this
new approach, and discuss some of its shortcomings. We use simulations to illustrate
the results and to form conjectures, getting numerical estimates for combinatorial,
topological, and geometric properties of weighted and unweighted Delaunay mosaics,
their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in
the mosaics."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The project in Chapter 2 has received funding from the European Research
Council (ERC) under the European Union's Horizon 2020 research and innovation programme
under grant agreement No. 638176. The project in Chapter 3 was funded in part by
the European Union (ERC-2021-COG 101045083 CoDiNA). The project in Chapter 4 has
received funding from the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha
and No 638176). It was also partially supported by the DFG Collaborative Research
Center TRR 109, 'Discretization in Geometry and Dynamics', through grant no. I02979-N35
of the Austrian Science Fund (FWF). Thank you for providing funds to support my
work.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
citation:
ama: Synak P. Methods for fluid simulation, surface tracking, and statistics of
non-manifold structures. 2025. doi:10.15479/AT-ISTA-19630
apa: Synak, P. (2025). Methods for fluid simulation, surface tracking, and statistics
of non-manifold structures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19630
chicago: Synak, Peter. “Methods for Fluid Simulation, Surface Tracking, and Statistics
of Non-Manifold Structures.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-19630.
ieee: P. Synak, “Methods for fluid simulation, surface tracking, and statistics
of non-manifold structures,” Institute of Science and Technology Austria, 2025.
ista: Synak P. 2025. Methods for fluid simulation, surface tracking, and statistics
of non-manifold structures. Institute of Science and Technology Austria.
mla: Synak, Peter. Methods for Fluid Simulation, Surface Tracking, and Statistics
of Non-Manifold Structures. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19630.
short: P. Synak, Methods for Fluid Simulation, Surface Tracking, and Statistics
of Non-Manifold Structures, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-04-29T09:39:34Z
date_published: 2025-04-29T00:00:00Z
date_updated: 2026-04-16T08:29:34Z
day: '29'
ddc:
- '519'
- '006'
degree_awarded: PhD
department:
- _id: ChWo
- _id: GradSch
doi: 10.15479/AT-ISTA-19630
ec_funded: 1
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date_updated: 2025-04-30T14:02:25Z
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creator: cchlebak
date_created: 2025-04-30T14:02:42Z
date_updated: 2025-04-30T15:49:16Z
file_id: '19634'
file_name: Thesis_PDFA_Heiss_Synak.pdf
file_size: 21319043
relation: main_file
file_date_updated: 2025-04-30T15:49:16Z
fulldoi: https://doi.org/10.15479/AT-ISTA-19630
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '106'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8135'
relation: part_of_dissertation
status: public
- id: '17219'
relation: part_of_dissertation
status: public
- id: '8384'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Methods for fluid simulation, surface tracking, and statistics of non-manifold
structures
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19702'
abstract:
- lang: eng
text: Moran Birth-death process is a standard stochastic process that is used to
model natural selection in spatially structured populations. A newly occurring
mutation that invades a population of residents can either fixate on the whole
population or it can go extinct due to random drift. The duration of the process
depends not only on the total population size n, but also on the spatial structure
of the population. In this work, we consider the Moran process with a single type
of individuals who invade and colonize an otherwise empty environment. Mathematically,
this corresponds to the setting where the residents have zero reproduction rate,
thus they never reproduce. The spatial structure is represented by a graph. We
present two main contributions. First, in contrast to the Moran process in which
residents do reproduce, we show that the colonization time is always at most a
polynomial function of the population size n. Namely, we show that colonization
always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify
the slowest graph where it takes exactly that many steps. Moreover, we establish
a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger
bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various
complications that one faces when attempting to measure fixation times and colonization
times in spatially structured populations, and we propose to measure the real
duration of the process, rather than counting the steps of the classic Moran process.
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Lenka
full_name: Kopfová, Lenka
id: 17691681-50b9-11ef-ad56-edf4cacb21b0
last_name: Kopfová
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. PLoS
computational biology. 2025;21(5):e1012868. doi:10.1371/journal.pcbi.1012868
apa: Kopfová, L., & Tkadlec, J. (2025). Colonization times in Moran process
on graphs. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012868
chicago: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process
on Graphs.” PLoS Computational Biology. Public Library of Science, 2025.
https://doi.org/10.1371/journal.pcbi.1012868.
ieee: L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,”
PLoS computational biology, vol. 21, no. 5. Public Library of Science,
p. e1012868, 2025.
ista: Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs.
PLoS computational biology. 21(5), e1012868.
mla: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on
Graphs.” PLoS Computational Biology, vol. 21, no. 5, Public Library of
Science, 2025, p. e1012868, doi:10.1371/journal.pcbi.1012868.
short: L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-09-30T12:34:03Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
doi: 10.1371/journal.pcbi.1012868
external_id:
arxiv:
- '2410.09476'
isi:
- '001481670600002'
file:
- access_level: open_access
checksum: 73e35151eebd5064972c5a07ffdf2b69
content_type: application/pdf
creator: dernst
date_created: 2025-05-19T07:45:31Z
date_updated: 2025-05-19T07:45:31Z
file_id: '19709'
file_name: 2025_PloSCompBio_Kopfova.pdf
file_size: 6805943
relation: main_file
success: 1
file_date_updated: 2025-05-19T07:45:31Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1012868
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: e1012868
publication: PLoS computational biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colonization times in Moran process on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19704'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular
labelling. Light microscopy is uniquely positioned to visualize specific molecules,
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach, owing to limitations in resolution, contrast and volumetric imaging
capability. Here we describe light-microscopy-based connectomics (LICONN). We
integrated specifically engineered hydrogel embedding and expansion with comprehensive
deep-learning-based segmentation and analysis of connectivity, thereby directly
incorporating molecular information into synapse-level reconstructions of brain
tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological
experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank S. Dorkenwald and P. Li for critical reading of the manuscript,
S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge
support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific
Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge
funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D.
and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft
für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s
Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions
Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation
programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open
access funding provided by Institute of Science and Technology (IST Austria).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- 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: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- 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: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic
reconstruction of mammalian brain tissue. Nature. 2025;642:398-410. doi:10.1038/s41586-025-08985-1
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction
of mammalian brain tissue. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08985-1
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based
Connectomic Reconstruction of Mammalian Brain Tissue.” Nature. Springer
Nature, 2025. https://doi.org/10.1038/s41586-025-08985-1.
ieee: M. Tavakoli et al., “Light-microscopy-based connectomic reconstruction
of mammalian brain tissue,” Nature, vol. 642. Springer Nature, pp. 398–410,
2025.
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain
tissue. Nature. 642, 398–410.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction
of Mammalian Brain Tissue.” Nature, vol. 642, Springer Nature, 2025, pp.
398–410, doi:10.1038/s41586-025-08985-1.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.
corr_author: '1'
date_created: 2025-05-18T22:02:51Z
date_published: 2025-06-12T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '12'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: Bio
- _id: GaNo
doi: 10.1038/s41586-025-08985-1
ec_funded: 1
external_id:
isi:
- '001483477000001'
pmid:
- '40335689'
file:
- access_level: open_access
checksum: ebc99d7108e728f46db0a009292675ef
content_type: application/pdf
creator: dernst
date_created: 2025-07-03T06:55:20Z
date_updated: 2025-07-03T06:55:20Z
file_id: '19959'
file_name: 2025_Nature_Tavakoli.pdf
file_size: 133201290
relation: main_file
success: 1
file_date_updated: 2025-07-03T06:55:20Z
fulldoi: https://doi.org/10.1038/s41586-025-08985-1
has_accepted_license: '1'
intvolume: ' 642'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 398-410
pmid: 1
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/
record:
- id: '18677'
relation: earlier_version
status: public
- id: '18697'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Light-microscopy-based connectomic reconstruction of mammalian brain tissue
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 642
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19738'
abstract:
- lang: eng
text: "Garbling is a fundamental cryptographic primitive, with numerous theoretical
and practical applications. Since the first construction by Yao (FOCS’82, ’86),
a line of work has concerned itself with reducing the communication and computational
complexity of that construction. One of the most efficient garbling schemes presently
is the ‘Half Gates’ scheme by Zahur, Rosulek, and Evans (Eurocrypt’15). Despite
its widespread adoption, the provable security of this scheme has been based on
assumptions whose only instantiations are in idealized models. For example, in
their original paper, Zahur, Rosulek, and Evans showed that hash functions satisfying
a notion called circular correlation robustness (CCR) suffice for this task, and
then proved that CCR secure hash functions can be instantiated in the random permutation
model.\r\nIn this work, we show how to securely instantiate the Half Gates scheme
in the standard model. To this end, we first show how this scheme can be securely
instantiated given a (family of) weak CCR hash function, a notion that we introduce.
Furthermore, we show how a weak CCR hash function can be used to securely instantiate
other efficient garbling schemes, namely the ones by Rosulek and Roy (Crypto’21)
and Heath (Eurocrypt’24). Thus we believe this notion to be of independent interest.\r\nFinally,
we construct such weak CCR hash functions using indistinguishability obfuscation
and one-way functions. The security proof of this construction constitutes our
main technical contribution. While our construction is not practical, it serves
as a proof of concept supporting the soundness of these garbling schemes, which
we regard to be particularly important given the recent initiative by NIST to
standardize garbling, and the optimizations in Half Gates being potentially adopted."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Anasuya
full_name: Acharya, Anasuya
last_name: Acharya
- first_name: Karen
full_name: Azari, Karen
last_name: Azari
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Dennis
full_name: Hofheinz, Dennis
last_name: Hofheinz
- first_name: Chethan
full_name: Kamath, Chethan
last_name: Kamath
citation:
ama: 'Acharya A, Azari K, Baig MA, Hofheinz D, Kamath C. Securely instantiating
‘Half Gates’ garbling in the standard model. In: 28th IACR International Conference
on Practice and Theory of Public-Key Cryptography. Vol 15677. Springer Nature;
2025:37-75. doi:10.1007/978-3-031-91829-2_2'
apa: 'Acharya, A., Azari, K., Baig, M. A., Hofheinz, D., & Kamath, C. (2025).
Securely instantiating ‘Half Gates’ garbling in the standard model. In 28th
IACR International Conference on Practice and Theory of Public-Key Cryptography
(Vol. 15677, pp. 37–75). Roros, Norway: Springer Nature. https://doi.org/10.1007/978-3-031-91829-2_2'
chicago: Acharya, Anasuya, Karen Azari, Mirza Ahad Baig, Dennis Hofheinz, and Chethan
Kamath. “Securely Instantiating ‘Half Gates’ Garbling in the Standard Model.”
In 28th IACR International Conference on Practice and Theory of Public-Key
Cryptography, 15677:37–75. Springer Nature, 2025. https://doi.org/10.1007/978-3-031-91829-2_2.
ieee: A. Acharya, K. Azari, M. A. Baig, D. Hofheinz, and C. Kamath, “Securely instantiating
‘Half Gates’ garbling in the standard model,” in 28th IACR International Conference
on Practice and Theory of Public-Key Cryptography, Roros, Norway, 2025, vol.
15677, pp. 37–75.
ista: 'Acharya A, Azari K, Baig MA, Hofheinz D, Kamath C. 2025. Securely instantiating
‘Half Gates’ garbling in the standard model. 28th IACR International Conference
on Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography,
LNCS, vol. 15677, 37–75.'
mla: Acharya, Anasuya, et al. “Securely Instantiating ‘Half Gates’ Garbling in the Standard
Model.” 28th IACR International Conference on Practice and Theory of Public-Key
Cryptography, vol. 15677, Springer Nature, 2025, pp. 37–75, doi:10.1007/978-3-031-91829-2_2.
short: A. Acharya, K. Azari, M.A. Baig, D. Hofheinz, C. Kamath, in:, 28th IACR International
Conference on Practice and Theory of Public-Key Cryptography, Springer Nature,
2025, pp. 37–75.
conference:
end_date: 2025-05-15
location: Roros, Norway
name: 'PKC: Public-Key Cryptography'
start_date: 2025-05-12
date_created: 2025-05-25T22:17:02Z
date_published: 2025-05-05T00:00:00Z
date_updated: 2025-06-02T07:01:45Z
day: '05'
department:
- _id: KrPi
- _id: GradSch
doi: 10.1007/978-3-031-91829-2_2
fulldoi: https://doi.org/10.1007/978-3-031-91829-2_2
intvolume: ' 15677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2025/281
month: '05'
oa: 1
oa_version: Preprint
page: 37-75
publication: 28th IACR International Conference on Practice and Theory of Public-Key
Cryptography
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031918285'
issn:
- 0302-9743
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Securely instantiating ‘Half Gates’ garbling in the standard model
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15677
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19778'
abstract:
- lang: eng
text: "A verifiable delay function VDF(x, T)->(y, π) maps an input x and time parameter
T to an output y together with an efficiently verifiable proof π certifying that
y was correctly computed. The function runs in T sequential steps, and it should
not be possible to compute y much faster than that. The only known practical VDFs
use sequential squaring in groups of unknown order as the sequential function,
i.e., y = x^2^T. There are two constructions for the proof of exponentiation (PoE)
certifying that y = x^2^T, with Wesolowski (Eurocrypt’19) having very short proofs,
but they are more expensive to compute and the soundness relies on stronger assumptions
than the PoE proposed by Pietrzak (ITCS’19).\r\nA recent application of VDFs by
Arun, Bonneau and Clark (Asiacrypt’22) are short-lived proofs and signatures,
which are proofs and signatures that are only sound for some time t, but after
that can be forged by anyone. For this they rely on “watermarkable VDFs”, where
the proof embeds a prover chosen watermark. To achieve stronger notions of proofs/signatures
with reusable forgeability, they rely on “zero-knowledge VDFs”, where instead
of the output y, one just proves knowledge of this output. The existing proposals
for watermarkable and zero-knowledge VDFs all build on Wesolowski’s PoE, for the
watermarkable VDFs there’s currently no security proof.\r\n\r\nIn this work we
give the first constructions that transform any PoEs in hidden order groups into
watermarkable VDFs and into zkVDFs, solving an open question by Arun et al. Unlike
our watermarkable VDF, the zkVDF (required for reusable forgeability) is not very
practical as the number of group elements in the proof is a security parameter.
To address this, we introduce the notion of zero-knowledge proofs of sequential
work (zkPoSW), a notion that relaxes zkVDFs by not requiring that the output is
unique. We show that zkPoSW are sufficient to construct proofs or signatures with
reusable forgeability, and construct efficient zkPoSW from any PoE, ultimately
achieving short lived proofs and signatures that improve upon Arun et al.’s construction
in several dimensions (faster forging times, arguably weaker assumptions).\r\nA
key idea underlying our constructions is to not directly construct a (watermarked
or zk) proof for y = x^2^T, but instead give a (watermarked or zk) proof for the
more basic statement that \r\nx^l, y^l satisfy x^l = x ^r, y^l = y^r for some
r, together with a normal PoE for y^l = (x^l)^2^T."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Charlotte
full_name: Hoffmann, Charlotte
id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7
last_name: Hoffmann
orcid: 0000-0003-2027-5549
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Hoffmann C, Pietrzak KZ. Watermarkable and zero-knowledge Verifiable Delay
Functions from any proof of exponentiation. In: 28th IACR International Conference
on Practice and Theory of Public-Key Cryptography. Vol 15674. Springer Nature;
2025:36-66. doi:10.1007/978-3-031-91820-9_2'
apa: 'Hoffmann, C., & Pietrzak, K. Z. (2025). Watermarkable and zero-knowledge
Verifiable Delay Functions from any proof of exponentiation. In 28th IACR International
Conference on Practice and Theory of Public-Key Cryptography (Vol. 15674,
pp. 36–66). Roros, Norway: Springer Nature. https://doi.org/10.1007/978-3-031-91820-9_2'
chicago: Hoffmann, Charlotte, and Krzysztof Z Pietrzak. “Watermarkable and Zero-Knowledge
Verifiable Delay Functions from Any Proof of Exponentiation.” In 28th IACR
International Conference on Practice and Theory of Public-Key Cryptography,
15674:36–66. Springer Nature, 2025. https://doi.org/10.1007/978-3-031-91820-9_2.
ieee: C. Hoffmann and K. Z. Pietrzak, “Watermarkable and zero-knowledge Verifiable
Delay Functions from any proof of exponentiation,” in 28th IACR International
Conference on Practice and Theory of Public-Key Cryptography, Roros, Norway,
2025, vol. 15674, pp. 36–66.
ista: 'Hoffmann C, Pietrzak KZ. 2025. Watermarkable and zero-knowledge Verifiable
Delay Functions from any proof of exponentiation. 28th IACR International Conference
on Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography,
LNCS, vol. 15674, 36–66.'
mla: Hoffmann, Charlotte, and Krzysztof Z. Pietrzak. “Watermarkable and Zero-Knowledge
Verifiable Delay Functions from Any Proof of Exponentiation.” 28th IACR International
Conference on Practice and Theory of Public-Key Cryptography, vol. 15674,
Springer Nature, 2025, pp. 36–66, doi:10.1007/978-3-031-91820-9_2.
short: C. Hoffmann, K.Z. Pietrzak, in:, 28th IACR International Conference on Practice
and Theory of Public-Key Cryptography, Springer Nature, 2025, pp. 36–66.
conference:
end_date: 2025-05-15
location: Roros, Norway
name: 'PKC: Public-Key Cryptography'
start_date: 2025-05-12
corr_author: '1'
date_created: 2025-06-03T07:30:21Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2026-04-16T09:11:09Z
day: '01'
department:
- _id: KrPi
- _id: GradSch
doi: 10.1007/978-3-031-91820-9_2
fulldoi: https://doi.org/10.1007/978-3-031-91820-9_2
intvolume: ' 15674'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ia.cr/2024/481
month: '01'
oa: 1
oa_version: Preprint
page: 36-66
publication: 28th IACR International Conference on Practice and Theory of Public-Key
Cryptography
publication_identifier:
eisbn:
- '9783031918209'
eissn:
- 1611-3349
isbn:
- '9783031918193'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20920'
relation: dissertation_contains
status: public
- id: '20556'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Watermarkable and zero-knowledge Verifiable Delay Functions from any proof
of exponentiation
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 15674
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19852'
abstract:
- lang: eng
text: "Technology involving hybrid superconductor–semiconductor materials is a promising
avenue for engineering quantum devices for information storage, manipulation,
and transmission. Proximity-induced superconducting correlations are an essential
part of such devices. While the proximity effect in the conduction band of common
semiconductors is well understood, its manifestation in confined hole gases, realized
for instance in germanium, is an active area of research. Lower-dimensional hole-based
systems, particularly in germanium, are emerging as an attractive platform for
a variety of solid-state quantum devices, due to their combination of efficient
spin and charge control and long coherence times. The recent experimental realization
of the proximity effect in germanium thus calls for a theoretical description
that is tailored to hole gases. In this work, we propose a simple model to describe
proximity-induced superconductivity in two-dimensional hole gases, incorporating
both the heavy-hole (HH) and light-hole (LH) bands. We start from the Luttinger–Kohn
model, introduce three parameters that characterize hopping across the superconductor–semiconductor
interface, and derive explicit intraband and interband effective pairing terms
for the HH and LH bands. Unlike previous approaches, our theory provides a quantitative
relationship between induced pairings and interface properties. Restricting our
general model to an experimentally relevant case where only the HH band crosses
the chemical potential, we predict the coexistence of \U0001D460-wave and \U0001D451-wave
singlet pairings, along with triplet-type pairings, and modified Zeeman and Rashba
spin–orbit couplings. Our results thus present a starting point for theoretical
modeling of quantum devices based on proximitized hole gases, fueling further
progress in quantum technology."
acknowledgement: We acknowledge useful discussions with Georgios Katsaros, Andrew
Higginbotham, and Oliver Schwarze. This research was funded in part by the Austrian
Science Fund (FWF) F 86, the European Research Council (Grant Agreement No. 856526),
and by the DFG Collaborative Research Center (CRC) 183 Project No. 277101999.
article_number: '214518'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Serafim
full_name: Babkin, Serafim
id: e63d75c3-72ef-11ef-b75a-e303e149911f
last_name: Babkin
- first_name: Benjamin
full_name: Joecker, Benjamin
last_name: Joecker
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
citation:
ama: Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. Superconducting proximity
effect in two-dimensional hole gases. Physical Review B. 2025;111(21).
doi:10.1103/k4jh-pnxy
apa: Babkin, S., Joecker, B., Flensberg, K., Serbyn, M., & Danon, J. (2025).
Superconducting proximity effect in two-dimensional hole gases. Physical Review
B. American Physical Society. https://doi.org/10.1103/k4jh-pnxy
chicago: Babkin, Serafim, Benjamin Joecker, Karsten Flensberg, Maksym Serbyn, and
Jeroen Danon. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.”
Physical Review B. American Physical Society, 2025. https://doi.org/10.1103/k4jh-pnxy.
ieee: S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, and J. Danon, “Superconducting
proximity effect in two-dimensional hole gases,” Physical Review B, vol.
111, no. 21. American Physical Society, 2025.
ista: Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. 2025. Superconducting
proximity effect in two-dimensional hole gases. Physical Review B. 111(21), 214518.
mla: Babkin, Serafim, et al. “Superconducting Proximity Effect in Two-Dimensional
Hole Gases.” Physical Review B, vol. 111, no. 21, 214518, American Physical
Society, 2025, doi:10.1103/k4jh-pnxy.
short: S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, J. Danon, Physical Review
B 111 (2025).
corr_author: '1'
date_created: 2025-06-19T16:54:54Z
date_published: 2025-06-18T00:00:00Z
date_updated: 2025-09-30T12:53:47Z
day: '18'
ddc:
- '530'
department:
- _id: MaSe
- _id: GradSch
doi: 10.1103/k4jh-pnxy
external_id:
arxiv:
- '2412.04084'
isi:
- '001514328000004'
file:
- access_level: open_access
checksum: fa8757f4780cfaeb51579c626284a8c1
content_type: application/pdf
creator: dernst
date_created: 2025-06-23T10:31:11Z
date_updated: 2025-06-23T10:31:11Z
file_id: '19869'
file_name: 2025_PhysReviewB_Babkin.pdf
file_size: 1719489
relation: main_file
success: 1
file_date_updated: 2025-06-23T10:31:11Z
fulldoi: https://doi.org/10.1103/k4jh-pnxy
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
issue: '21'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 34a7f947-11ca-11ed-8bc3-c5dc2bbaae25
grant_number: F8609
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Probing
topology in circuits and quantum materials'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconducting proximity effect in two-dimensional hole gases
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 111
year: '2025'
...
---
OA_place: publisher
_id: '19853'
abstract:
- lang: eng
text: "The internal dynamical properties of red giant stars have been explored extensively
in recent\r\nyears as a result of the increase in high precision data availability
from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite),
and in this exploration, it has been\r\ndiscovered that some of these stars are
not behaving as expected. Red giants are stars that have\r\nevolved off of the
main sequence after having completed fusing hydrogen into helium in their\r\ncore.
Observational data shows that the cores are rotating significantly slower than
models can\r\nrecreate consistently across evolutionary stages. This discrepancy
has prompted investigation\r\ninto the efficiency of angular momentum transport
mechanisms and mixing processes including\r\nmeridional circulation, shear instability,
internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc.,
to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology,
is a powerful tool as it is the only\r\nway in which the deep stellar interior
can be probed and subsequently characterized; this is\r\npossible as global oscillations
modulating the stellar surface are effected by internal processes.\r\nFor red
giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes;
resonating in the radiative interior) couple to create mixed modes. These\r\nmixed
modes give access to the otherwise hidden stellar interior as g-modes couple to
p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal
magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology
and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1
will display a global asymmetric frequency shift of its azimuthal components;
where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted
by two\r\ndifferent power laws, respectively. And the other being a reduced visibility
of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting
with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed
dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated
studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted;
one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen
the dipole mixed mode amplitudes are severely reduced in many of the suppressed
stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars,
that is, red giant stars presenting with suppressed dipole mixed modes in select
parts of\r\ntheir power spectra rather than across the entire spectra, will be
the subject of this study as\r\nthe respective mode amplitudes are still visible
at high frequencies.\r\nAs such, this study will search for asymmetric frequency
shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the
aim here is to investigate if both\r\nmode suppression and magnetic shifting of
dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse
the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand
perform a Bayesian fit of the parameters with the simulated data on the star KIC
6975038,\r\na target with partially suppressed dipolar mode amplitudes identified
in the literature, to fit its\r\nmagnetic parameters. I present a novel method
to model the stellar power spectra of\r\npartially suppressed red giants by application
of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With
the results of this study I aim at constraining\r\nthe cause of this partial dipole
mode amplitude suppression, allowing for more detailed\r\nstudies regarding their
astrophysical nature. Furthermore, the long term hope for the method\r\nused in
this study will be to expand the sample of partially suppressed red giants and
fit their\r\nasteroseismic parameters accordingly."
acknowledgement: "I would like to give thanks to myself for my hard work on this document.
This paper includes data collected by the Kepler mission and obtained from the MAST
data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the
Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is
operated by the Association of\r\nUniversities for Research in Astronomy, Inc.,
under NASA contract NAS 5–26555.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Kanah
full_name: Smith, Kanah
id: 7703505d-3211-11ee-a6a9-a2ab9d936c15
last_name: Smith
citation:
ama: Smith K. Exploring internal magnetism in partially suppressed red giant stars.
2025. doi:10.15479/AT-ISTA-19853
apa: Smith, K. (2025). Exploring internal magnetism in partially suppressed red
giant stars. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19853
chicago: Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red
Giant Stars.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19853.
ieee: K. Smith, “Exploring internal magnetism in partially suppressed red giant
stars,” Institute of Science and Technology Austria, 2025.
ista: Smith K. 2025. Exploring internal magnetism in partially suppressed red giant
stars. Institute of Science and Technology Austria.
mla: Smith, Kanah. Exploring Internal Magnetism in Partially Suppressed Red Giant
Stars. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19853.
short: K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant
Stars, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-06-20T13:27:08Z
date_published: 2025-10-08T00:00:00Z
date_updated: 2026-04-07T12:01:37Z
day: '08'
ddc:
- '520'
degree_awarded: MS
department:
- _id: GradSch
- _id: LiBu
doi: 10.15479/AT-ISTA-19853
file:
- access_level: closed
checksum: 80d241d11b69af771c1fab0998be4f19
content_type: application/zip
creator: ksmith
date_created: 2025-10-08T08:01:42Z
date_updated: 2025-10-08T09:45:33Z
file_id: '20434'
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file_size: 8263624
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creator: ksmith
date_created: 2025-10-09T14:38:57Z
date_updated: 2025-10-09T14:38:57Z
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file_name: 2025_Smith_Kanah_Thesis.pdf
file_size: 9748339
relation: main_file
success: 1
file_date_updated: 2025-10-09T14:38:57Z
fulldoi: https://doi.org/10.15479/AT-ISTA-19853
has_accepted_license: '1'
keyword:
- asteroseismology
- stellar physics
- red giant
- magnetism
- suppressed
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '38'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
title: Exploring internal magnetism in partially suppressed red giant stars
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
_id: '19885'
abstract:
- lang: eng
text: This .zip file contains the data to reproduce the figures and supplementary
figures of "Automated All-RF Tuning for Spin Qubit Readout and Control" by Cornelius
Carlsson and Jaime Saez-Mollejo et al.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: 'The authors would like to thank Barnaby van Straaten, Jonas Schuff,
Daniel Jirovec and Hanifa Tidjani for fruitful discussions. This research was supported
by the Scientific Service Units of ISTA through resources provided by the MIBA Machine
Shop and the Nanofabrication Facility. G.K. acknowledges support from the NOMIS
Foundation, the HORIZON-RIA (project no. 101069515) and the FWF Projects (DOIs:
10.55776/F86 and 10.55776/I5060). N.A. acknowledges support from the European Research
Council (grant agreement 948932), and the Royal Society (grant no. URF/R1/191150).
This project received support from the US Army Research Office (ARO) under Award
No. W911NF-24-2-0043. C.C. acknowledges support from the UKRI Doctoral Training
Partnership related to EP/W524311/1 (project ref. 2887634).'
article_processing_charge: No
author:
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
citation:
ama: Saez Mollejo J. Automated All-RF Tuning for Spin Qubit Readout and Control.
2025. doi:10.15479/AT:ISTA:19885
apa: Saez Mollejo, J. (2025). Automated All-RF Tuning for Spin Qubit Readout and
Control. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:19885
chicago: Saez Mollejo, Jaime. “Automated All-RF Tuning for Spin Qubit Readout and
Control.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:19885.
ieee: J. Saez Mollejo, “Automated All-RF Tuning for Spin Qubit Readout and Control.”
Institute of Science and Technology Austria, 2025.
ista: Saez Mollejo J. 2025. Automated All-RF Tuning for Spin Qubit Readout and Control,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:19885.
mla: Saez Mollejo, Jaime. Automated All-RF Tuning for Spin Qubit Readout and
Control. Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:19885.
short: J. Saez Mollejo, (2025).
contributor:
- contributor_type: researcher
first_name: Cornelius
last_name: Carlsson
- contributor_type: researcher
first_name: 'Federico '
last_name: Fedele
- contributor_type: researcher
first_name: Stefano
last_name: Calcaterra
- contributor_type: researcher
first_name: ' Daniel '
last_name: Chrastina
- contributor_type: researcher
first_name: 'Giovanni '
last_name: Isella
- contributor_type: researcher
first_name: Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- contributor_type: researcher
first_name: Natalia
last_name: Ares
corr_author: '1'
date_created: 2025-06-24T06:56:03Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2025-07-01T07:19:26Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:19885
file:
- access_level: open_access
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creator: jsaezmol
date_created: 2025-06-24T15:14:13Z
date_updated: 2025-06-24T15:14:13Z
file_id: '19893'
file_name: DatasetsPaper.zip
file_size: 3404814792
relation: main_file
success: 1
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checksum: 21840ceac04d677a799b8e5bd919804f
content_type: text/plain
creator: jsaezmol
date_created: 2025-06-25T07:11:52Z
date_updated: 2025-06-25T07:11:52Z
file_id: '19899'
file_name: README.txt
file_size: 622
relation: main_file
success: 1
file_date_updated: 2025-06-25T07:11:52Z
fulldoi: https://doi.org/10.15479/AT:ISTA:19885
has_accepted_license: '1'
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
publisher: Institute of Science and Technology Austria
status: public
title: Automated All-RF Tuning for Spin Qubit Readout and Control
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '20149'
abstract:
- lang: eng
text: "Immune responses depend on the coordinated and efficient migration of leukocytes.
These\r\ncells, which are embedded and tightly confined within tissues, must navigate
and traverse\r\ndiverse and complex three-dimensional environments. Leukocytes
adapt their locomotory\r\nbehavior to the mechanical, geometrical, and biochemical
characteristics of their\r\nsurroundings. In low-density environments, where the
pore size of the interstitial matrix\r\nallows free passage, these cells position
the nucleus directly behind the lamellipodium, the\r\nprotrusive actin structure
that forms the leading front of the cell. In this configuration, they\r\nuse the
nucleus as a gauge to identify the path of least resistance.\r\nHere, we show
that in high-density environments, where the pore size precludes free passage\r\nof
the cell body, leukocytes reposition the microtubule-organizing center (MTOC)
and\r\nassociated organelles in front of the nucleus. In this configuration, they
use actin structures\r\nprotruding orthogonally to the direction of migration
in order to open a path for the cell body.\r\nWe identify two distinct actin populations
that serve this purpose at different subcellular\r\nlocalizations. At the leading
edge, local indentation of the plasma membrane leads to\r\nrecruitment of the
Wiskott-Aldrich syndrome protein (WASp), which, via Arp2/3, results in\r\nthe
formation of individual actin foci. At the cell body, actin polymerization is
triggered by\r\nDOCK8, a Cdc42 exchange factor, resulting in the formation of
a central actin pool.\r\nWe demonstrate that the central and peripheral actin
pools are functionally communicating\r\nand that depletion of the central actin
pool leads to increased actin accumulation at the cell\r\nfront, resulting in
excessive extension of the leading edge."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: NanoFab
acknowledgement: "I would like to acknowledge the\r\nfinancial support of the European
Research Council through the ERC-SyG grant “Pushing from\r\nwithin: Control of cell
shape, integrity and motility by cytoskeletal pushing forces”\r\n(01071793), which
made this research possible. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Patricia
full_name: Dos Reis Rodrigues, Patricia
id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F
last_name: Dos Reis Rodrigues
orcid: 0000-0003-1681-508X
citation:
ama: Dos Reis Rodrigues P. Coordination of protrusive forces in immune cell migration
. 2025. doi:10.15479/AT-ISTA-20149
apa: Dos Reis Rodrigues, P. (2025). Coordination of protrusive forces in immune
cell migration . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20149
chicago: Dos Reis Rodrigues, Patricia. “Coordination of Protrusive Forces in Immune
Cell Migration .” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20149.
ieee: P. Dos Reis Rodrigues, “Coordination of protrusive forces in immune cell migration
,” Institute of Science and Technology Austria, 2025.
ista: Dos Reis Rodrigues P. 2025. Coordination of protrusive forces in immune cell
migration . Institute of Science and Technology Austria.
mla: Dos Reis Rodrigues, Patricia. Coordination of Protrusive Forces in Immune
Cell Migration . Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20149.
short: P. Dos Reis Rodrigues, Coordination of Protrusive Forces in Immune Cell Migration
, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-08T09:18:02Z
date_published: 2025-08-08T00:00:00Z
date_updated: 2026-04-28T13:26:50Z
day: '08'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/AT-ISTA-20149
file:
- access_level: open_access
checksum: fda8a1070667c3562263f4867609b41b
content_type: application/pdf
creator: prodrigu
date_created: 2025-08-27T12:59:10Z
date_updated: 2025-08-27T12:59:10Z
file_id: '20232'
file_name: 2025_ReisRodrigues_Patricia_Thesis.pdf
file_size: 63885565
relation: main_file
success: 1
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checksum: e8b65affcbce846a926454df4b2867b9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: prodrigu
date_created: 2025-08-27T13:00:30Z
date_updated: 2025-08-27T13:02:28Z
file_id: '20233'
file_name: 2025_ReisRodrigues_Patricia_Thesis.docx
file_size: 50483434
relation: source_file
file_date_updated: 2025-08-27T13:02:28Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20149
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '114'
project:
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10703'
relation: part_of_dissertation
status: public
- id: '20082'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Coordination of protrusive forces in immune cell migration '
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20184'
abstract:
- lang: eng
text: Specialized DNA polymerases facilitate various cellular processes. Despite
extensive research, the mutagenic effects of these error-prone enzymes on genomes
are not fully understood. Here we show that Pol IV promotes genomic instability
in Pseudomonas aeruginosa by misincorporating oxidized guanine nucleotides. This
activity led to a distinctive mutational signature, characterized by A-to-C transversions
occurring preferentially at AT sites flanked by a 5’G and/or 3’C. Furthermore,
Pol IV preferentially targeted pathogenicity genes located at specific chromosomal
locations near the replication termination region and rRNA-encoding operons. Half
of the mutation events catalyzed by Pol IV impaired gene function. This can be
attributed to the bias of Pol IV for mutating codons with its preferred sequence
contexts, leading to substitutions to unreactive alanine and glycine residues.
Remarkably, mutation signatures identified for Pol IV were found in clinical isolate
genomes of P. aeruginosa, providing compelling evidence for its role in genetic
diversification during pathogen adaptation.
acknowledgement: "This work was supported by the Secretaría de Ciencia y Técnica (33620230100926CB),
Universidad Nacional de Córdoba; and the Agencia Nacional de Promoción Científica
y Técnica (PICT 2018-4527).\r\n\r\n"
article_number: '1148'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sofía D.
full_name: Castell, Sofía D.
last_name: Castell
- first_name: Consuelo M.
full_name: Fernandez, Consuelo M.
last_name: Fernandez
- first_name: Ignacio N.
full_name: Tumas, Ignacio N.
last_name: Tumas
- first_name: Lucía M.
full_name: Margara, Lucía M.
last_name: Margara
- first_name: Maria C
full_name: Miserendino, Maria C
id: 273e0cbd-72f0-11ef-b75a-f9f932e292fa
last_name: Miserendino
- first_name: Danilo G.
full_name: Ceschin, Danilo G.
last_name: Ceschin
- first_name: Roberto J.
full_name: Pezza, Roberto J.
last_name: Pezza
- first_name: Mariela R.
full_name: Monti, Mariela R.
last_name: Monti
citation:
ama: Castell SD, Fernandez CM, Tumas IN, et al. The low-fidelity DNA Pol IV accelerates
evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications
Biology. 2025;8. doi:10.1038/s42003-025-08589-5
apa: Castell, S. D., Fernandez, C. M., Tumas, I. N., Margara, L. M., Miserendino,
M. C., Ceschin, D. G., … Monti, M. R. (2025). The low-fidelity DNA Pol IV accelerates
evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-025-08589-5
chicago: Castell, Sofía D., Consuelo M. Fernandez, Ignacio N. Tumas, Lucía M. Margara,
Maria C Miserendino, Danilo G. Ceschin, Roberto J. Pezza, and Mariela R. Monti.
“The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas
Aeruginosa.” Communications Biology. Springer Nature, 2025. https://doi.org/10.1038/s42003-025-08589-5.
ieee: S. D. Castell et al., “The low-fidelity DNA Pol IV accelerates evolution
of pathogenicity genes in Pseudomonas aeruginosa,” Communications Biology,
vol. 8. Springer Nature, 2025.
ista: Castell SD, Fernandez CM, Tumas IN, Margara LM, Miserendino MC, Ceschin DG,
Pezza RJ, Monti MR. 2025. The low-fidelity DNA Pol IV accelerates evolution of
pathogenicity genes in Pseudomonas aeruginosa. Communications Biology. 8, 1148.
mla: Castell, Sofía D., et al. “The Low-Fidelity DNA Pol IV Accelerates Evolution
of Pathogenicity Genes in Pseudomonas Aeruginosa.” Communications Biology,
vol. 8, 1148, Springer Nature, 2025, doi:10.1038/s42003-025-08589-5.
short: S.D. Castell, C.M. Fernandez, I.N. Tumas, L.M. Margara, M.C. Miserendino,
D.G. Ceschin, R.J. Pezza, M.R. Monti, Communications Biology 8 (2025).
date_created: 2025-08-17T22:01:35Z
date_published: 2025-08-02T00:00:00Z
date_updated: 2025-09-30T14:18:46Z
day: '02'
ddc:
- '570'
department:
- _id: PaSc
- _id: GradSch
doi: 10.1038/s42003-025-08589-5
external_id:
isi:
- '001541878500001'
pmid:
- '40753298'
fulldoi: https://doi.org/10.1038/s42003-025-08589-5
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s42003-025-08589-5
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in
Pseudomonas aeruginosa
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2025'
...