---
_id: '14032'
abstract:
- lang: eng
text: Arrays of Josephson junctions are governed by a competition between superconductivity
and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature
resistance when interactions exceed a critical level. Here we report a study of
the transport and microwave response of Josephson arrays with interactions exceeding
this level. Contrary to expectations, we observe that the array resistance drops
dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and
then saturates at low temperature. Applying a magnetic field, we eventually observe
a transition to a highly resistive regime. These observations can be understood
within a theoretical picture that accounts for the effect of thermal fluctuations
on the insulating phase. On the basis of the agreement between experiment and
theory, we suggest that apparent superconductivity in our Josephson arrays arises
from melting the zero-temperature insulator.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman
for helpful feedback on the paper. This research was supported by the Scientific
Service Units of IST Austria through resources provided by the MIBA Machine Shop
and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N
(S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and
a NOMIS foundation research grant (J.M.F. and A.P.H.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
orcid: 0000-0003-1144-2763
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a
melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635.
doi:10.1038/s41567-023-02161-w
apa: Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M.,
Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted
insulator in Josephson junction arrays. Nature Physics. Springer Nature.
https://doi.org/10.1038/s41567-023-02161-w
chicago: Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia,
Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity
from a Melted Insulator in Josephson Junction Arrays.” Nature Physics.
Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.
ieee: S. Mukhopadhyay et al., “Superconductivity from a melted insulator
in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature,
pp. 1630–1635, 2023.
ista: Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM,
Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson
junction arrays. Nature Physics. 19, 1630–1635.
mla: Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson
Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35,
doi:10.1038/s41567-023-02161-w.
short: S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M.
Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.
date_created: 2023-08-11T07:41:17Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-29T11:27:49Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: AnHi
- _id: JoFi
doi: 10.1038/s41567-023-02161-w
ec_funded: 1
external_id:
isi:
- '001054563800006'
file:
- access_level: open_access
checksum: 1fc86d71bfbf836e221c1e925343adc5
content_type: application/pdf
creator: dernst
date_created: 2024-01-29T11:25:38Z
date_updated: 2024-01-29T11:25:38Z
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file_size: 1977706
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has_accepted_license: '1'
intvolume: ' 19'
isi: 1
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1630-1635
project:
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344
name: Protected states of quantum matter
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconductivity from a melted insulator in Josephson junction arrays
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '14058'
abstract:
- lang: eng
text: "Females and males across species are subject to divergent selective pressures
arising\r\nfrom di↵erent reproductive interests and ecological niches. This often
translates into a\r\nintricate array of sex-specific natural and sexual selection
on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic
sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution
of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual
dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications
of the genetic networks ultimately linked to sex-determining\r\ntranscription
factors. Although much empirical and theoretical evidence supports this\r\nstandard
picture of the molecular basis of sexual conflict resolution, there still are
a\r\nfew open questions regarding the complex array of selective forces driving
phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms
underlying sexspecific adaptation. I address some of these open questions in my
PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within
populations,\r\nas a response to the temporal and spatial changes in sex-specific
selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific
phenotypic variation along\r\nthree life stages and across populations spanning
the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm,
in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns
lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying
the observed transcriptomic variation? I\r\naddress this question by examining
the sex- and tissue-specific expression variation in\r\nnewly-generated datasets
of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster.
I additionally used two complementary approaches for the study of the\r\ngenetic
basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe
thesis.\r\nThird, how does intersex correlation, thought to be one of the main
aspects constraining the ability for the two sexes to decouple, interact with
the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing
selection, mutation and drift\r\nto formalize common intuition regarding the patterns
of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth
Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides
useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic
layers of sex-specific variation,\r\nand contributes to our general understanding
of the dynamics of sexual dimorphism\r\nevolution."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058'
apa: 'Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058'
chicago: 'Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14058.'
ieee: 'G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria.'
mla: 'Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14058.'
short: 'G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and
Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.'
date_created: 2023-08-15T10:20:40Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-12-13T12:15:36Z
day: '15'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/at:ista:14058
ec_funded: 1
file:
- access_level: closed
checksum: 4e44e169f2724ee8c9324cd60bcc2b71
content_type: application/zip
creator: gpuixeus
date_created: 2023-08-16T18:15:17Z
date_updated: 2023-08-17T06:55:24Z
file_id: '14075'
file_name: Thesis_latex_forpdfa.zip
file_size: 10891454
relation: source_file
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checksum: e10b04cd8f3fecc0d9ef6e6868b6e1e8
content_type: application/pdf
creator: gpuixeus
date_created: 2023-08-18T10:47:55Z
date_updated: 2023-08-18T10:47:55Z
file_id: '14079'
file_name: PhDThesis_PuixeuG.pdf
file_size: 19856686
relation: main_file
success: 1
file_date_updated: 2023-08-18T10:47:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '230'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication_identifier:
isbn:
- 978-3-99078-035-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9803'
relation: research_data
status: public
- id: '12933'
relation: research_data
status: public
- id: '6831'
relation: part_of_dissertation
status: public
- id: '14077'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization
of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14077'
abstract:
- lang: eng
text: "The regulatory architecture of gene expression is known to differ substantially
between sexes in Drosophila, but most studies performed\r\nso far used whole-body
data and only single crosses, which may have limited their scope to detect patterns
that are robust across tissues\r\nand biological replicates. Here, we use allele-specific
gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster
inbred lines to quantify cis- and trans-regulatory variation in heads and gonads
of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that
female and male heads, as well as ovaries, have a similar regulatory architecture.
On the other hand,\r\ntestes display more and substantially different cis-regulatory
effects, suggesting that sex differences in the regulatory architecture that\r\nhave
been previously observed may largely derive from testis-specific effects. We also
examine the difference in cis-regulatory variation\r\nof genes across different
levels of sex bias in gonads and heads. Consistent with the idea that intersex
correlations constrain expression\r\nand can lead to sexual antagonism, we find
more cis variation in unbiased and moderately biased genes in heads. In ovaries,
reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis
variants acting on these genes in males do not lead to changes in ovary\r\nexpression.
Finally, we examine the dominance patterns of gene expression and find that sex-
and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation
are highly variable across biological crosses, although these were performed in
highly controlled\r\nexperimental conditions. This highlights the importance of
using various genetic backgrounds to infer generalizable patterns."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank members of the Vicoso Group for comments on the manuscript,
the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers
for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy
of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received
funding from the European Union’s Horizon 2020 research and innovation program under
the Marie Skłodowska-Curie Grant (agreement no. 665385).
article_processing_charge: Yes
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121'
apa: 'Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation
of cis and trans regulation of gene expression in heads and gonads of Drosophila
melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121'
chicago: 'Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation
of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila
Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023.
https://doi.org/10.1093/g3journal/jkad121.'
ieee: 'G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis
and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,”
G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press,
2023.'
ista: 'Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and
trans regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 13(8).'
mla: 'Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation
of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes,
Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.'
short: 'G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).'
date_created: 2023-08-18T06:52:14Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:15:37Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
- _id: GradSch
doi: 10.1093/g3journal/jkad121
ec_funded: 1
external_id:
isi:
- '001002997200001'
file:
- access_level: open_access
checksum: c62e29fc7c5efbf8356f4c60cab4a2d1
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T09:00:19Z
date_updated: 2023-11-07T09:00:19Z
file_id: '14498'
file_name: 2023_G3_Puixeu.pdf
file_size: 845642
relation: main_file
success: 1
file_date_updated: 2023-11-07T09:00:19Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '8'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
- 2160-1836
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '12933'
relation: research_data
status: public
- id: '14058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sex-specific estimation of cis and trans regulation of gene expression in heads
and gonads of Drosophila melanogaster
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2023'
...
---
_id: '14087'
abstract:
- lang: eng
text: Polar active matter of self-propelled particles sustain spontaneous flows
through the full-integer topological defects. We study theoretically the incompressible
flow profiles around ±1 defects induced by polar and dipolar active forces. We
show that dipolar forces induce vortical flows around the +1 defect, while the
flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow
changes its chirality near the +1 defect core in the absence of the friction with
a substrate. We show analytically that the flow induced by polar active forces
is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while
it becomes uniform in the far-field. For a pair of oppositely charged defects,
this polar flow contributes to a mutual interaction force that depends only on
the orientation of the defect pair relative to the background polarization, and
that enhances defect pair annihilation. This is in contradiction with the effect
of dipolar active forces which decay inversely proportional with the defect separation
distance. As such, our analyses reveals a long-ranged mechanism for the pairwise
interaction between topological defects in polar active matter.
acknowledgement: J. Rø and L. A. acknowledge support from the Research Council of
Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab).
A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142
and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European
Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however
those of the authors 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.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Jonas
full_name: Rønning, Jonas
last_name: Rønning
- first_name: Julian B
full_name: Renaud, Julian B
id: 7af6767d-14eb-11ed-b536-a32449ae867c
last_name: Renaud
- first_name: Amin
full_name: Doostmohammadi, Amin
last_name: Doostmohammadi
- first_name: Luiza
full_name: Angheluta, Luiza
last_name: Angheluta
citation:
ama: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and
dynamics of full-integer topological defects in polar active matter. Soft Matter.
2023;39:7513-7527. doi:10.1039/d3sm00316g
apa: Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023).
Spontaneous flows and dynamics of full-integer topological defects in polar active
matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g
chicago: Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta.
“Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active
Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g.
ieee: J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous
flows and dynamics of full-integer topological defects in polar active matter,”
Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.
ista: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows
and dynamics of full-integer topological defects in polar active matter. Soft
Matter. 39, 7513–7527.
mla: Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological
Defects in Polar Active Matter.” Soft Matter, vol. 39, Royal Society of
Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g.
short: J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39
(2023) 7513–7527.
date_created: 2023-08-20T22:01:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-01-30T12:49:24Z
day: '01'
ddc:
- '540'
department:
- _id: GradSch
doi: 10.1039/d3sm00316g
external_id:
arxiv:
- '2303.07063'
isi:
- '001035766100001'
file:
- access_level: open_access
checksum: b936747170d0b708172b518078c4081a
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:48:24Z
date_updated: 2024-01-30T12:48:24Z
file_id: '14908'
file_name: 2023_SoftMatter_Ronning.pdf
file_size: 7660662
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:48:24Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 7513-7527
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous flows and dynamics of full-integer topological defects in polar
active matter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '14226'
abstract:
- lang: eng
text: "We introduce the notion of a Faustian interchange in a 1-parameter family
of smooth\r\nfunctions to generalize the medial axis to critical points of index
larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating
such\r\ngeneralized medial axes."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
citation:
ama: Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226
apa: Stephenson, E. R. (2023). Generalizing medial axes with homology switches.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226
chicago: Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.
ieee: E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute
of Science and Technology Austria, 2023.
ista: Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute
of Science and Technology Austria.
mla: Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.
short: E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute
of Science and Technology Austria, 2023.
date_created: 2023-08-24T13:01:18Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2024-02-26T23:30:04Z
day: '24'
ddc:
- '500'
degree_awarded: MS
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:14226
file:
- access_level: closed
checksum: 453caf851d75c3478c10ed09bd242a91
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-08-24T13:02:49Z
date_updated: 2024-02-26T23:30:03Z
embargo_to: open_access
file_id: '14227'
file_name: documents-export-2023-08-24.zip
file_size: 15501411
relation: source_file
- access_level: open_access
checksum: 7349d29963d6695e555e171748648d9a
content_type: application/pdf
creator: cchlebak
date_created: 2023-08-24T13:03:42Z
date_updated: 2024-02-26T23:30:03Z
embargo: 2024-02-25
file_id: '14228'
file_name: thesis_pdf_a.pdf
file_size: 6854783
relation: main_file
file_date_updated: 2024-02-26T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '43'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
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: Generalizing medial axes with homology switches
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14260'
abstract:
- lang: eng
text: "This paper presents Lincheck, a new practical and user-friendly framework
for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck
provides a simple and declarative way to write concurrent tests: instead of describing
how to perform the test, users specify what to test by declaring all the operations
to examine; the framework automatically handles the rest. As a result, tests written
with Lincheck are concise and easy to understand. The framework automatically
generates a set of concurrent scenarios, examines them using stress-testing or
bounded model checking, and verifies that the results of each invocation are correct.
Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow
trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo
the best of our knowledge, Lincheck is the first production-ready tool on the
JVM that offers such a simple way of writing concurrent tests, without requiring
special skills or expertise. We successfully integrated Lincheck in the development
process of several large projects, such as Kotlin Coroutines, and identified new
bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque
and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is
used in most of the synchronization primitives. We believe that Lincheck can significantly
improve the quality and productivity of concurrent algorithms research and development
and become the state-of-the-art tool for checking their correctness."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Maria
full_name: Sokolova, Maria
last_name: Sokolova
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. In: 35th International
Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169.
doi:10.1007/978-3-031-37706-8_8'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. In 35th International Conference on Computer Aided Verification
(Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” In 35th International Conference on Computer Aided Verification
, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM,” in 35th
International Conference on Computer Aided Verification , Paris, France, 2023,
vol. 13964, pp. 156–169.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM. 35th International
Conference on Computer Aided Verification . CAV: Computer Aided Verification,
LNCS, vol. 13964, 156–169.'
mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM.” 35th International Conference on Computer Aided Verification
, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th
International Conference on Computer Aided Verification , Springer Nature, 2023,
pp. 156–169.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2024-02-27T07:46:52Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
file:
- access_level: open_access
checksum: c346016393123a0a2338ad4d976f61bc
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:16:25Z
date_updated: 2023-09-06T08:16:25Z
file_id: '14275'
file_name: 2023_LNCS_Koval.pdf
file_size: 421408
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:16:25Z
has_accepted_license: '1'
intvolume: ' 13964'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 156-169
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14995'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on JVM'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13964
year: '2023'
...
---
_id: '14261'
abstract:
- lang: eng
text: In this work, a generalized, adapted Numerov implementation capable of determining
band structures of periodic quantum systems is outlined. Based on the input potential,
the presented approach numerically solves the Schrödinger equation in position
space at each momentum space point. Thus, in addition to the band structure, the
method inherently provides information about the state functions and probability
densities in position space at each momentum space point considered. The generalized,
adapted Numerov framework provided reliable estimates for a variety of increasingly
complex test suites in one, two, and three dimensions. The accuracy of the proposed
methodology was benchmarked against results obtained for the analytically solvable
Kronig-Penney model. Furthermore, the presented numerical solver was applied to
a model potential representing a 2D optical lattice being a challenging application
relevant, for example, in the field of quantum computing.
acknowledgement: Financial supports for this work via a PhD scholarship for J. Gamper
issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike
Tanzer) are gratefully acknowledged. The computational results presented have been
achieved (in part) using the HPC infrastructure of the University of Innsbruck.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jakob
full_name: Gamper, Jakob
last_name: Gamper
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Alexander K.H.
full_name: Weiss, Alexander K.H.
last_name: Weiss
- first_name: Thomas S.
full_name: Hofer, Thomas S.
last_name: Hofer
citation:
ama: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave
functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707
apa: Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023).
Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems. Journal of Physical Chemistry Letters. American Chemical
Society. https://doi.org/10.1021/acs.jpclett.3c01707
chicago: Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas
S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations
of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-,
Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry
Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.
ieee: J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position
space wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems,”
Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical
Society, pp. 7395–7403, 2023.
ista: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space
wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 14(33), 7395–7403.
mla: Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure
Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation
for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical
Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403,
doi:10.1021/acs.jpclett.3c01707.
short: J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical
Chemistry Letters 14 (2023) 7395–7403.
date_created: 2023-09-03T22:01:16Z
date_published: 2023-08-11T00:00:00Z
date_updated: 2023-09-06T11:04:31Z
day: '11'
ddc:
- '530'
- '540'
department:
- _id: GradSch
doi: 10.1021/acs.jpclett.3c01707
external_id:
isi:
- '001048165800001'
pmid:
- '37566743'
file:
- access_level: open_access
checksum: 637454e2b3a357498d8d622d241c4bf6
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:32:39Z
date_updated: 2023-09-06T07:32:39Z
file_id: '14272'
file_name: 2023_JourPhysChemistry_Gamper.pdf
file_size: 4986859
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:32:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 7395-7403
pmid: 1
publication: Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2023'
...
---
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
file:
- access_level: closed
checksum: 87eef11fbc5c7df0826f12a3a629b444
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pradler
date_created: 2023-10-04T10:11:53Z
date_updated: 2023-10-04T10:28:35Z
file_id: '14390'
file_name: PhD Thesis_Philipp Radler_20231004.docx
file_size: 114932847
relation: source_file
- access_level: closed
checksum: 3253e099b7126469d941fd9419d68b4f
content_type: application/pdf
creator: pradler
date_created: 2023-10-04T10:11:21Z
date_updated: 2023-10-04T10:28:35Z
embargo: 2024-10-04
embargo_to: open_access
file_id: '14391'
file_name: PhD Thesis_Philipp Radler_20231004.pdf
file_size: 37838778
relation: main_file
file_date_updated: 2023-10-04T10:28:35Z
has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
month: '09'
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
- id: '10934'
relation: research_data
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Spatiotemporal signaling during assembly of the bacterial divisome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14323'
abstract:
- lang: eng
text: Morphogens are signaling molecules that are known for their prominent role
in pattern formation within developing tissues. In addition to patterning, morphogens
also control tissue growth. However, the underlying mechanisms are poorly understood.
We studied the role of morphogens in regulating tissue growth in the developing
vertebrate neural tube. In this system, opposing morphogen gradients of Shh and
BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations
in these morphogen pathways result in alterations in tissue growth and cell cycle
progression, however, it has been unclear what cellular process is affected. To
address this, we analysed the rates of cell proliferation and cell death in mouse
mutants in which signaling is perturbed, as well as in chick neural plate explants
exposed to defined concentrations of signaling activators or inhibitors. Our results
indicated that the rate of cell proliferation was not altered in these assays.
By contrast, both the Shh and BMP signaling pathways had profound effects on neural
progenitor survival. Our results indicate that these pathways synergise to promote
cell survival within neural progenitors. Consistent with this, we found that progenitors
within the intermediate region of the neural tube, where the combined levels of
Shh and BMP are the lowest, are most prone to cell death when signaling activity
is inhibited. In addition, we found that downregulation of Shh results in increased
apoptosis within the roof plate, which is the dorsal source of BMP ligand production.
This revealed a cross-interaction between the Shh and BMP morphogen signaling
pathways that may be relevant for understanding how gradients scale in neural
tubes with different overall sizes. We further studied the mechanism acting downstream
of Shh in cell survival regulation using genetic and genomic approaches. We propose
that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether,
our study points to a novel role of opposing morphogen gradients in tissue size
regulation and provides new insights into complex interactions between Shh and
BMP signaling gradients in the neural tube.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
citation:
ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP
in the developing spinal cord. 2023. doi:10.15479/at:ista:14323
apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by
Shh and BMP in the developing spinal cord. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:14323
chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival
by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14323.
ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and
BMP in the developing spinal cord,” Institute of Science and Technology Austria,
2023.
ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh
and BMP in the developing spinal cord. Institute of Science and Technology Austria.
mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by
Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:14323.
short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and
BMP in the Developing Spinal Cord, Institute of Science and Technology Austria,
2023.
date_created: 2023-09-13T10:07:18Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2024-03-07T15:02:59Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
doi: 10.15479/at:ista:14323
file:
- access_level: closed
checksum: bd83596869c814b24aeff7077d031c0e
content_type: application/pdf
creator: kkuzmicz
date_created: 2023-09-13T09:52:52Z
date_updated: 2023-09-13T10:08:25Z
embargo: 2025-03-13
embargo_to: open_access
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file_name: PhDThesis_KK_final_pdfA.pdf
file_size: 10147911
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creator: kkuzmicz
date_created: 2023-09-13T09:53:29Z
date_updated: 2023-09-13T09:53:29Z
file_id: '14325'
file_name: thesis_KK_final_corrections_092023.docx
file_size: 103980668
relation: source_file
file_date_updated: 2023-09-13T10:08:25Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa_version: Published Version
page: '151'
project:
- _id: 267AF0E4-B435-11E9-9278-68D0E5697425
name: The role of morphogens in the regulation of neural tube growth
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7883'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal
cord
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14343'
abstract:
- lang: eng
text: The total energy of an eigenstate in a composite quantum system tends to be
distributed equally among its constituents. We identify the quantum fluctuation
around this equipartition principle in the simplest disordered quantum system
consisting of linear combinations of Wigner matrices. As our main ingredient,
we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for
general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary
deformation.
acknowledgement: "G.C. and L.E. gratefully acknowledge many discussions with Dominik
Schröder at the preliminary stage of this project, especially his essential contribution
to identify the correct generalisation of traceless observables to the deformed
Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’
No. 101020331."
article_number: e74
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Oleksii
full_name: Kolupaiev, Oleksii
id: 149b70d4-896a-11ed-bdf8-8c63fd44ca61
last_name: Kolupaiev
citation:
ama: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the
equipartition principle for Wigner matrices. Forum of Mathematics, Sigma.
2023;11. doi:10.1017/fms.2023.70
apa: Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian
fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics,
Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70
chicago: Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev.
“Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum
of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70.
ieee: G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations
in the equipartition principle for Wigner matrices,” Forum of Mathematics,
Sigma, vol. 11. Cambridge University Press, 2023.
ista: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations
in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma.
11, e74.
mla: Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle
for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge
University Press, 2023, doi:10.1017/fms.2023.70.
short: G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics,
Sigma 11 (2023).
date_created: 2023-09-17T22:01:09Z
date_published: 2023-08-23T00:00:00Z
date_updated: 2023-12-13T12:24:23Z
day: '23'
ddc:
- '510'
department:
- _id: LaEr
- _id: GradSch
doi: 10.1017/fms.2023.70
ec_funded: 1
external_id:
arxiv:
- '2301.05181'
isi:
- '001051980200001'
file:
- access_level: open_access
checksum: eb747420e6a88a7796fa934151957676
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T11:09:35Z
date_updated: 2023-09-20T11:09:35Z
file_id: '14352'
file_name: 2023_ForumMathematics_Cipolloni.pdf
file_size: 852652
relation: main_file
success: 1
file_date_updated: 2023-09-20T11:09:35Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gaussian fluctuations in the equipartition principle for Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2023'
...
---
_id: '14374'
abstract:
- lang: eng
text: "Superconductivity has many important applications ranging from levitating
trains over qubits to MRI scanners. The phenomenon is successfully modeled by
Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory
has been studied extensively for systems without boundary. However, little is
known in the presence of boundaries. With the help of numerical methods physicists
observed that the critical temperature may increase in the presence of a boundary.
The goal of this thesis is to understand the influence of boundaries on the critical
temperature in BCS theory and to give a first rigorous justification of these
observations. On the way, we also study two-body Schrödinger operators on domains
with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS
theory is based on a non-linear functional, where the minimizer indicates whether
the system is superconducting or in the normal, non-superconducting state. By
considering the Hessian of the BCS functional at the normal state, one can analyze
whether the normal state is possibly a minimum of the BCS functional and estimate
the critical temperature. The Hessian turns out to be a linear operator resembling
a Schrödinger operator for two interacting particles, but with more complicated
kinetic energy. As a first step, we study the two-body Schrödinger operator in
the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that
the addition of a boundary can create new eigenvalues, which correspond to the
two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need
to understand superconductivity in the translation invariant setting. While in
three dimensions this has been extensively studied, there is no mathematical literature
for the one and two dimensional cases. In dimensions one and two, we compute the
weak coupling asymptotics of the critical temperature and the energy gap in the
translation invariant setting. We also prove that their ratio is independent of
the microscopic details of the model in the weak coupling limit; this property
is referred to as universality.\r\n\r\nIn the third part, we study the critical
temperature of superconductors in the presence of boundaries. We start by considering
the one-dimensional case of a half-line with contact interaction. Then, we generalize
the results to generic interactions and half-spaces in one, two and three dimensions.
Finally, we compare the critical temperature of a quarter space in two dimensions
to the critical temperatures of a half-space and of the full space."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374
apa: Roos, B. (2023). Boundary superconductivity in BCS theory. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374
chicago: Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.
ieee: B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science
and Technology Austria, 2023.
ista: Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science
and Technology Austria.
mla: Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of
Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.
short: B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and
Technology Austria, 2023.
date_created: 2023-09-28T14:23:04Z
date_published: 2023-09-30T00:00:00Z
date_updated: 2023-10-27T10:37:30Z
day: '30'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:14374
ec_funded: 1
file:
- access_level: open_access
checksum: ef039ffc3de2cb8dee5b14110938e9b6
content_type: application/pdf
creator: broos
date_created: 2023-10-06T11:35:56Z
date_updated: 2023-10-06T11:35:56Z
file_id: '14398'
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file_size: 2365702
relation: main_file
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checksum: 81dcac33daeefaf0111db52f41bb1fd0
content_type: application/x-zip-compressed
creator: broos
date_created: 2023-10-06T11:38:01Z
date_updated: 2023-10-06T11:38:01Z
file_id: '14399'
file_name: Version5.zip
file_size: 4691734
relation: source_file
file_date_updated: 2023-10-06T11:38:01Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '206'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13207'
relation: part_of_dissertation
status: public
- id: '10850'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: Boundary superconductivity in BCS theory
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14421'
abstract:
- lang: eng
text: Only recently has it been possible to construct a self-adjoint Hamiltonian
that involves the creation of Dirac particles at a point source in 3d space. Its
definition makes use of an interior-boundary condition. Here, we develop for this
Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously)
construct a Markov jump process $(Q_t)_{t\in\mathbb{R}}$ in the configuration
space of a variable number of particles that is $|\psi_t|^2$-distributed at every
time t and follows Bohmian trajectories between the jumps. The jumps correspond
to particle creation or annihilation events and occur either to or from a configuration
with a particle located at the source. The process is the natural analog of Bell's
jump process, and a central piece in its construction is the determination of
the rate of particle creation. The construction requires an analysis of the asymptotic
behavior of the Bohmian trajectories near the source. We find that the particle
reaches the source with radial speed 0, but orbits around the source infinitely
many times in finite time before absorption (or after emission).
acknowledgement: J H gratefully acknowledges partial financial support by the ERC
Advanced Grant 'RMTBeyond' No. 101020331.
article_number: '445201'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Roderich
full_name: Tumulka, Roderich
last_name: Tumulka
citation:
ama: 'Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source.
Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62'
apa: 'Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles
at a point source. Journal of Physics A: Mathematical and Theoretical.
IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62'
chicago: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles
at a Point Source.” Journal of Physics A: Mathematical and Theoretical.
IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.'
ieee: 'S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point
source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no.
44. IOP Publishing, 2023.'
ista: 'Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point
source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.'
mla: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles
at a Point Source.” Journal of Physics A: Mathematical and Theoretical,
vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62.'
short: 'S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical
56 (2023).'
date_created: 2023-10-12T12:42:53Z
date_published: 2023-10-11T00:00:00Z
date_updated: 2023-12-13T13:01:25Z
day: '11'
ddc:
- '510'
department:
- _id: GradSch
- _id: LaEr
doi: 10.1088/1751-8121/acfe62
ec_funded: 1
external_id:
arxiv:
- '2211.16606'
isi:
- '001080908000001'
file:
- access_level: open_access
checksum: 5b68de147dd4c608b71a6e0e844d2ce9
content_type: application/pdf
creator: dernst
date_created: 2023-10-16T07:07:24Z
date_updated: 2023-10-16T07:07:24Z
file_id: '14429'
file_name: 2023_JourPhysics_Henheik.pdf
file_size: 721399
relation: main_file
success: 1
file_date_updated: 2023-10-16T07:07:24Z
has_accepted_license: '1'
intvolume: ' 56'
isi: 1
issue: '44'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_identifier:
eissn:
- 1751-8121
issn:
- 1751-8113
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Creation rate of Dirac particles at a point source
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2023'
...
---
_id: '14422'
abstract:
- lang: eng
text: "Animals exhibit a remarkable ability to learn and remember new behaviors,
skills, and associations throughout their lifetime. These capabilities are made
possible thanks to a variety of\r\nchanges in the brain throughout adulthood,
regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons—
and specifically changes in the connections between neurons, the\r\nsynapses,
were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom
past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity.
Understanding how a myriad of biochemical processes operating at individual\r\nsynapses
can somehow work in concert to give rise to meaningful changes in behavior is
a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental
search for the precise plasticity mechanisms at play in the brain\r\nis daunting,
as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches
have thus been the default method to probe the plasticity-behavior connection.
Such\r\nstudies attempt to extract unifying principles across synapses and model
all observed synaptic\r\nchanges using plasticity rules: equations that govern
the evolution of synaptic strengths across\r\ntime in neuronal network models.
These rules can use many relevant quantities to determine\r\nthe magnitude of
synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction
potentials, the recent neuronal activity levels, the state of neighboring synapses,
etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced
to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis,
we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe
explore whether a numerical approach could automatically discover the plasticity
rules\r\nthat elicit desired behaviors in large networks of interconnected neurons.
This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity
rules which themselves will make\r\nneuronal networks learn how to solve a desired
task. We first write all the potential plasticity\r\nmechanisms to consider using
a single expression with adjustable parameters. We then optimize\r\nthese plasticity
parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto
involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe
show that these automated approaches are powerful tools, able to complement established\r\nanalytical
methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic,
spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity
rules that reliably elicit memory-related behaviors. Our approaches allow for
more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies
of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity
in spiking network models.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
citation:
ama: 'Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422'
apa: 'Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity
rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422'
chicago: 'Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.'
ieee: 'B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute
of Science and Technology Austria, 2023.'
ista: 'Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules.
Institute of Science and Technology Austria.'
mla: 'Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.'
short: 'B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute
of Science and Technology Austria, 2023.'
date_created: 2023-10-12T14:13:25Z
date_published: 2023-10-12T00:00:00Z
date_updated: 2023-10-18T09:20:56Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TiVo
doi: 10.15479/at:ista:14422
ec_funded: 1
file:
- access_level: closed
checksum: 7f636555eae7803323df287672fd13ed
content_type: application/pdf
creator: cchlebak
date_created: 2023-10-12T14:53:50Z
date_updated: 2023-10-12T14:54:52Z
embargo: 2024-10-12
embargo_to: open_access
file_id: '14424'
file_name: Confavreux_Thesis_2A.pdf
file_size: 30599717
relation: main_file
- access_level: closed
checksum: 725e85946db92290a4583a0de9779e1b
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-10-18T07:38:34Z
date_updated: 2023-10-18T07:56:08Z
file_id: '14440'
file_name: Confavreux Thesis.zip
file_size: 68406739
relation: source_file
file_date_updated: 2023-10-18T07:56:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa_version: Published Version
page: '148'
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9633'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
title: 'Synapseek: Meta-learning synaptic plasticity rules'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14425'
abstract:
- lang: eng
text: 'Water adsorption and dissociation processes on pristine low-index TiO2 interfaces
are important but poorly understood outside the well-studied anatase (101) and
rutile (110). To understand these, we construct three sets of machine learning
potentials that are simultaneously applicable to various TiO2 surfaces, based
on three density-functional-theory approximations. Here we show the water dissociation
free energies on seven pristine TiO2 surfaces, and predict that anatase (100),
anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase
(101) and rutile (100) have mostly molecular adsorption, while the simulations
of rutile (110) sensitively depend on the slab thickness and molecular adsorption
is preferred with thick slabs. Moreover, using an automated algorithm, we reveal
that these surfaces follow different types of atomistic mechanisms for proton
transfer and water dissociation: one-step, two-step, or both. These mechanisms
can be rationalized based on the arrangements of water molecules on the different
surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces
react with water in distinct ways, and cannot be represented using just the low-energy
anatase (101) and rutile (110) surfaces.'
acknowledgement: F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre
(CSCS) for the generous allocation of CPU hours via production project s1108 at
the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge
Tier-2 system operated by the University of Cambridge Research Computing Service
funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing
Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank
the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab
Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie grant agreement No 101034413.
article_number: '6131'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
- first_name: Felix
full_name: Wodaczek, Felix
id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e
last_name: Wodaczek
orcid: 0009-0000-1457-795X
- first_name: Keyang
full_name: Liu, Keyang
last_name: Liu
- first_name: Frederick
full_name: Stein, Frederick
last_name: Stein
- first_name: Jürg
full_name: Hutter, Jürg
last_name: Hutter
- first_name: Ji
full_name: Chen, Ji
last_name: Chen
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation
on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations.
Nature Communications. 2023;14. doi:10.1038/s41467-023-41865-8
apa: Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., & Cheng,
B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2
surfaces from machine learning molecular dynamics simulations. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41865-8
chicago: Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter,
Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine
Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41865-8.
ieee: Z. Zeng et al., “Mechanistic insight on water dissociation on pristine
low-index TiO2 surfaces from machine learning molecular dynamics simulations,”
Nature Communications, vol. 14. Springer Nature, 2023.
ista: Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic
insight on water dissociation on pristine low-index TiO2 surfaces from machine
learning molecular dynamics simulations. Nature Communications. 14, 6131.
mla: Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine
Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.”
Nature Communications, vol. 14, 6131, Springer Nature, 2023, doi:10.1038/s41467-023-41865-8.
short: Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature
Communications 14 (2023).
date_created: 2023-10-15T22:01:10Z
date_published: 2023-10-02T00:00:00Z
date_updated: 2023-12-13T13:02:07Z
day: '02'
ddc:
- '540'
- '000'
department:
- _id: BiCh
- _id: GradSch
doi: 10.1038/s41467-023-41865-8
ec_funded: 1
external_id:
arxiv:
- '2303.07433'
isi:
- '001084354900008'
pmid:
- '37783698'
file:
- access_level: open_access
checksum: 7d1dffd36b672ec679f08f70ce79da87
content_type: application/pdf
creator: dernst
date_created: 2023-10-16T07:34:49Z
date_updated: 2023-10-16T07:34:49Z
file_id: '14432'
file_name: 2023_NatureComm_Zeng.pdf
file_size: 3194116
relation: main_file
success: 1
file_date_updated: 2023-10-16T07:34:49Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/TiO2-water
scopus_import: '1'
status: public
title: Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces
from machine learning molecular dynamics simulations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14466'
abstract:
- lang: eng
text: The first long-lived turbulent structures observable in planar shear flows
take the form of localized stripes, inclined with respect to the mean flow direction.
The dynamics of these stripes is central to transition, and recent studies proposed
an analogy to directed percolation where the stripes’ proliferation is ultimately
responsible for the turbulence becoming sustained. In the present study we focus
on the internal stripe dynamics as well as on the eventual stripe expansion, and
we compare the underlying mechanisms in pressure- and shear-driven planar flows,
respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities
of the overall laminar–turbulence patterns, the stripe proliferation processes
in the two cases are fundamentally different. Starting from the growth and sustenance
of individual stripes, we find that in plane-Couette flow new streaks are created
stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation
is deterministic and occurs locally at the downstream tip. Because of the up/downstream
symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and
two strong laminar turbulent interfaces. These differences in symmetry as well
as in internal growth give rise to two fundamentally different stripe splitting
mechanisms. In plane-Poiseuille flow splitting is connected to the elongational
growth of the original stripe, and it results from a break-off/shedding of the
stripe's tail. In plane-Couette flow splitting follows from a broadening of the
original stripe and a division along the stripe into two slimmer stripes.
acknowledgement: E.M. acknowledges funding from the ISTplus fellowship programme.
G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH).
article_number: A21
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes
in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
2023;974. doi:10.1017/jfm.2023.780
apa: Marensi, E., Yalniz, G., & Hof, B. (2023). Dynamics and proliferation of
turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid
Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2023.780
chicago: Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation
of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal
of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2023.780.
ieee: E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows,” Journal of Fluid Mechanics,
vol. 974. Cambridge University Press, 2023.
ista: Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
974, A21.
mla: Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in
Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics,
vol. 974, A21, Cambridge University Press, 2023, doi:10.1017/jfm.2023.780.
short: E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023).
date_created: 2023-10-30T09:32:28Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2024-02-15T09:06:23Z
day: '10'
ddc:
- '530'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1017/jfm.2023.780
external_id:
arxiv:
- '2212.12406'
isi:
- '001088363700001'
file:
- access_level: open_access
checksum: 17c64c1fb0d5f73252364bf98b0b9e1a
content_type: application/pdf
creator: dernst
date_created: 2024-02-15T09:05:21Z
date_updated: 2024-02-15T09:05:21Z
file_id: '14996'
file_name: 2023_JourFluidMechanics_Marensi.pdf
file_size: 2804641
relation: main_file
success: 1
file_date_updated: 2024-02-15T09:05:21Z
has_accepted_license: '1'
intvolume: ' 974'
isi: 1
keyword:
- turbulence
- transition to turbulence
- patterns
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette
flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 974
year: '2023'
...
---
_id: '14485'
abstract:
- lang: eng
text: "Batching is a technique that stores multiple keys/values in each node of
a data structure. In sequential search data structures, batching reduces latency
by reducing the number of cache misses and shortening the chain of pointers to
dereference. Applying batching to concurrent data structures is challenging, because
it is difficult to maintain the search property and keep contention low in the
presence of batching.\r\nIn this paper, we present a general methodology for leveraging
batching in concurrent search data structures, called BatchBoost. BatchBoost builds
a search data structure from distinct \"data\" and \"index\" layers. The data
layer’s purpose is to store a batch of key/value pairs in each of its nodes. The
index layer uses an unmodified concurrent search data structure to route operations
to a position in the data layer that is \"close\" to where the corresponding key
should exist. The requirements on the index and data layers are low: with minimal
effort, we were able to compose three highly scalable concurrent search data structures
based on three original data structures as the index layers with a batched version
of the Lazy List as the data layer. The resulting BatchBoost data structures provide
significant performance improvements over their original counterparts."
alternative_title:
- LIPIcs
article_number: '35'
article_processing_charge: Yes
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- first_name: Michael
full_name: Anoprenko, Michael
last_name: Anoprenko
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Michael
full_name: Spear, Michael
last_name: Spear
citation:
ama: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost:
Universal batching for concurrent data structures. In: 37th International Symposium
on Distributed Computing. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.DISC.2023.35'
apa: 'Aksenov, V., Anoprenko, M., Fedorov, A., & Spear, M. (2023). Brief announcement:
BatchBoost: Universal batching for concurrent data structures. In 37th International
Symposium on Distributed Computing (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2023.35'
chicago: 'Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear.
“Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.”
In 37th International Symposium on Distributed Computing, Vol. 281. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.DISC.2023.35.'
ieee: 'V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement:
BatchBoost: Universal batching for concurrent data structures,” in 37th International
Symposium on Distributed Computing, L’Aquila, Italy, 2023, vol. 281.'
ista: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost:
Universal batching for concurrent data structures. 37th International Symposium
on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol.
281, 35.'
mla: 'Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching
for Concurrent Data Structures.” 37th International Symposium on Distributed
Computing, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.DISC.2023.35.'
short: V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium
on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
conference:
end_date: 2023-10-13
location: L'Aquila, Italy
name: 'DISC: Symposium on Distributed Computing'
start_date: 2023-10-09
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-11-07T07:48:01Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
doi: 10.4230/LIPIcs.DISC.2023.35
file:
- access_level: open_access
checksum: d9f8d2915cccdf2df5905b7cd1b4a560
content_type: application/pdf
creator: dernst
date_created: 2023-11-06T11:45:21Z
date_updated: 2023-11-06T11:45:21Z
file_id: '14492'
file_name: 2023_LIPIcs_Aksenov.pdf
file_size: 646665
relation: main_file
success: 1
file_date_updated: 2023-11-06T11:45:21Z
has_accepted_license: '1'
intvolume: ' 281'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: 37th International Symposium on Distributed Computing
publication_identifier:
isbn:
- '9783959773010'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: BatchBoost: Universal batching for concurrent data structures'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2023'
...
---
_id: '14506'
abstract:
- lang: eng
text: "Payment channel networks are a promising approach to improve the scalability
bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel
networks are\r\nefficiency and privacy. Payment channel networks improve efficiency
by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes
in the network, avoiding\r\nthe lengthy process of consensus on the blockchain.
Transacting over payment channel\r\nnetworks also improves privacy as these transactions
are not broadcast to the blockchain.\r\nDespite the influx of recent protocols
built on top of payment channel networks and\r\ntheir analysis, a common shortcoming
of many of these protocols is that they typically\r\nfocus only on either improving
efficiency or privacy, but not both. Another limitation\r\non the efficiency front
is that the models used to model actions, costs and utilities of\r\nusers are
limited or come with unrealistic assumptions.\r\nThis thesis aims to address some
of the shortcomings of recent protocols and algorithms\r\non payment channel networks,
particularly in their privacy and efficiency aspects. We\r\nfirst present a payment
route discovery protocol based on hub labelling and private\r\ninformation retrieval
that hides the route query and is also efficient. We then present\r\na rebalancing
protocol that formulates the rebalancing problem as a linear program\r\nand solves
the linear program using multiparty computation so as to hide the channel\r\nbalances.
The rebalancing solution as output by our protocol is also globally optimal.\r\nWe
go on to develop more realistic models of the action space, costs, and utilities
of\r\nboth existing and new users that want to join the network. In each of these
settings,\r\nwe also develop algorithms to optimise the utility of these users
with good guarantees\r\non the approximation and competitive ratios."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis.
2023. doi:10.15479/14506
apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel
network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506
chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel
Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.
ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network
analysis,” Institute of Science and Technology Austria, 2023.
ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network
analysis. Institute of Science and Technology Austria.
mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network
Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.
short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis,
Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T08:10:43Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2025-07-14T09:09:52Z
day: '10'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/14506
ec_funded: 1
file:
- access_level: closed
checksum: 521c72818d720a52b377207b2ee87b6a
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-11-23T10:29:55Z
date_updated: 2023-11-23T10:29:55Z
file_id: '14598'
file_name: thesis_yeo.zip
file_size: 3037720
relation: source_file
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checksum: 0ed5d16899687aecf13d843c9878c9f2
content_type: application/pdf
creator: cchlebak
date_created: 2023-11-23T10:30:08Z
date_updated: 2023-11-23T10:30:08Z
file_id: '14599'
file_name: thesis_yeo.pdf
file_size: 2717256
relation: main_file
success: 1
file_date_updated: 2023-11-23T10:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '162'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9969'
relation: part_of_dissertation
status: public
- id: '14490'
relation: part_of_dissertation
status: public
- id: '13238'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Advances in efficiency and privacy in payment channel network analysis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14510'
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
citation:
ama: Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. 2023. doi:10.15479/at:ista:14510
apa: Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during
endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510
chicago: Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.
ieee: N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis
in plants,” Institute of Science and Technology Austria, 2023.
ista: Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. Institute of Science and Technology Austria.
mla: Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14510.
short: N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis
in Plants, Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T09:10:06Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2024-03-25T23:30:25Z
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keyword:
- Clathrin-Mediated Endocytosis
- vesicle scission
- Dynamin-Related Protein 2
- SH3P2
- TPLATE complex
- Total internal reflection fluorescence microscopy
- Arabidopsis thaliana
language:
- iso: eng
month: '11'
oa_version: Published Version
page: '180'
project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-037-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
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relation: part_of_dissertation
status: public
- id: '8139'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Mechanism of clathrin-coated vesicle formation during endocytosis in plants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14530'
abstract:
- lang: eng
text: 'Most motions of many-body systems at any scale in nature with sufficient
degrees of freedom tend to be chaotic; reaching from the orbital motion of planets,
the air currents in our atmosphere, down to the water flowing through our pipelines
or the movement of a population of bacteria. To the observer it is therefore intriguing
when a moving collective exhibits order. Collective motion of flocks of birds,
schools of fish or swarms of self-propelled particles or robots have been studied
extensively over the past decades but the mechanisms involved in the transition
from chaos to order remain unclear. Here, the interactions, that in most systems
give rise to chaos, sustain order. In this thesis we investigate mechanisms that
preserve, destabilize or lead to the ordered state. We show that endothelial cells
migrating in circular confinements transition to a collective rotating state and
concomitantly synchronize the frequencies of nucleating actin waves within individual
cells. Consequently, the frequency dependent cell migration speed uniformizes
across the population. Complementary to the WAVE dependent nucleation of traveling
actin waves, we show that in leukocytes the actin polymerization depending on
WASp generates pushing forces locally at stationary patches. Next, in pipe flows,
we study methods to disrupt the self--sustaining cycle of turbulence and therefore
relaminarize the flow. While we find in pulsating flow conditions that turbulence
emerges through a helical instability during the decelerating phase. Finally,
we show quantitatively in brain slices of mice that wild-type control neurons
can compensate the migratory deficits of a genetically modified neuronal sub--population
in the developing cortex. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
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full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
citation:
ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530
apa: Riedl, M. (2023). Synchronization in collectively moving active matter.
Institute of Science and Technology Austria. https://doi.org/10.15479/14530
chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.
ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute
of Science and Technology Austria, 2023.
ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute
of Science and Technology Austria.
mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter.
Institute of Science and Technology Austria, 2023, doi:10.15479/14530.
short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute
of Science and Technology Austria, 2023.
date_created: 2023-11-15T09:59:03Z
date_published: 2023-11-16T00:00:00Z
date_updated: 2023-11-30T10:55:13Z
day: '16'
ddc:
- '530'
- '570'
degree_awarded: PhD
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- _id: GradSch
- _id: MiSi
doi: 10.15479/14530
file:
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file_size: 36743942
relation: main_file
success: 1
file_date_updated: 2023-11-15T09:52:54Z
has_accepted_license: '1'
keyword:
- Synchronization
- Collective Movement
- Active Matter
- Cell Migration
- Active Colloids
language:
- iso: eng
month: '11'
oa: 1
oa_version: Updated Version
page: '260'
publication_identifier:
issn:
- 2663 - 337X
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status: public
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status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Synchronization in collectively moving active matter
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14539'
abstract:
- lang: eng
text: "Stochastic systems provide a formal framework for modelling and quantifying
uncertainty in systems and have been widely adopted in many application domains.
Formal\r\nverification and control of finite state stochastic systems, a subfield
of formal methods\r\nalso known as probabilistic model checking, is well studied.
In contrast, formal verification and control of infinite state stochastic systems
have received comparatively\r\nless attention. However, infinite state stochastic
systems commonly arise in practice.\r\nFor instance, probabilistic models that
contain continuous probability distributions such\r\nas normal or uniform, or
stochastic dynamical systems which are a classical model for\r\ncontrol under
uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis
is to contribute to laying theoretical and algorithmic foundations\r\nof fully
automated formal verification and control of infinite state stochastic systems,\r\nwith
a particular focus on systems that may be executed over a long or infinite time.\r\nWe
consider formal verification of infinite state stochastic systems in the setting
of\r\nstatic analysis of probabilistic programs and formal control in the setting
of controller\r\nsynthesis in stochastic dynamical systems. For both problems,
we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a.
quantitative) reachability and\r\nsafety analysis applicable to infinite time
horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a.
qualitative) reachability analysis for both problems.\r\nFinally, for formal controller
synthesis in stochastic dynamical systems, we present a\r\nnovel framework for
learning neural network control policies in stochastic dynamical\r\nsystems with
formal guarantees on correctness with respect to quantitative reachability,\r\nsafety
or reach-avoid specifications.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: Zikelic D. Automated verification and control of infinite state stochastic
systems. 2023. doi:10.15479/14539
apa: Zikelic, D. (2023). Automated verification and control of infinite state
stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539
chicago: Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic
Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539.
ieee: D. Zikelic, “Automated verification and control of infinite state stochastic
systems,” Institute of Science and Technology Austria, 2023.
ista: Zikelic D. 2023. Automated verification and control of infinite state stochastic
systems. Institute of Science and Technology Austria.
mla: Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic
Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539.
short: D. Zikelic, Automated Verification and Control of Infinite State Stochastic
Systems, Institute of Science and Technology Austria, 2023.
date_created: 2023-11-15T13:39:10Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2025-07-14T09:10:10Z
day: '15'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi: 10.15479/14539
ec_funded: 1
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month: '11'
oa: 1
oa_version: Published Version
page: '256'
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-036-7
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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- id: '12000'
relation: part_of_dissertation
status: public
- id: '12511'
relation: part_of_dissertation
status: public
- id: '14600'
relation: part_of_dissertation
status: public
- id: '14601'
relation: part_of_dissertation
status: public
- id: '9644'
relation: part_of_dissertation
status: public
- id: '10414'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Automated verification and control of infinite state stochastic systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
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short: CC BY-NC-SA (4.0)
type: dissertation
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...