---
_id: '13175'
abstract:
- lang: eng
text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13175
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:13175.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-06-30T08:07:43Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-10-29T09:11:06Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:13175
ec_funded: 1
file:
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content_type: application/pdf
creator: cchlebak
date_created: 2023-06-30T08:17:25Z
date_updated: 2023-06-30T08:17:25Z
file_id: '13176'
file_name: thesis_pdfa.pdf
file_size: 18688376
relation: main_file
success: 1
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checksum: c3b45317ae58e0527533f98c202d81b7
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-07-06T11:35:15Z
date_updated: 2023-07-06T11:35:15Z
file_id: '13196'
file_name: thesis.zip
file_size: 37847025
relation: source_file
file_date_updated: 2023-07-06T11:35:15Z
has_accepted_license: '1'
keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '202'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12900'
relation: old_edition
status: public
- id: '9114'
relation: part_of_dissertation
status: public
- id: '10924'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13207'
abstract:
- lang: eng
text: We consider the linear BCS equation, determining the BCS critical temperature,
in the presence of a boundary, where Dirichlet boundary conditions are imposed.
In the one-dimensional case with point interactions, we prove that the critical
temperature is strictly larger than the bulk value, at least at weak coupling.
In particular, the Cooper-pair wave function localizes near the boundary, an effect
that cannot be modeled by effective Neumann boundary conditions on the order parameter
as often imposed in Ginzburg–Landau theory. We also show that the relative shift
in critical temperature vanishes if the coupling constant either goes to zero
or to infinity.
acknowledgement: We thank Egor Babaev for encouraging us to study this problem, and
Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the
European Union’s Horizon 2020 research and innovation programme under the ERC grant
agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model.
Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439
apa: Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity
in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439
chicago: Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity
in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439.
ieee: C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS
model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540,
2023.
ista: Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS
model. Journal of Spectral Theory. 12(4), 1507–1540.
mla: Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal
of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439.
short: C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.
date_created: 2023-07-10T16:35:45Z
date_published: 2023-05-18T00:00:00Z
date_updated: 2023-10-27T10:37:29Z
day: '18'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.4171/JST/439
ec_funded: 1
external_id:
arxiv:
- '2201.08090'
isi:
- '000997933500008'
file:
- access_level: open_access
checksum: 5501da33be010b5c81440438287584d5
content_type: application/pdf
creator: alisjak
date_created: 2023-07-11T08:19:15Z
date_updated: 2023-07-11T08:19:15Z
file_id: '13208'
file_name: 2023_EMS_Hainzl.pdf
file_size: 304619
relation: main_file
success: 1
file_date_updated: 2023-07-11T08:19:15Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1507–1540
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Spectral Theory
publication_identifier:
eissn:
- 1664-0403
issn:
- 1664-039X
publication_status: published
publisher: EMS Press
quality_controlled: '1'
related_material:
record:
- id: '14374'
relation: dissertation_contains
status: public
status: public
title: Boundary superconductivity in the BCS model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2023'
...
---
_id: '13221'
abstract:
- lang: eng
text: The safety-liveness dichotomy is a fundamental concept in formal languages
which plays a key role in verification. Recently, this dichotomy has been lifted
to quantitative properties, which are arbitrary functions from infinite words
to partially-ordered domains. We look into harnessing the dichotomy for the specific
classes of quantitative properties expressed by quantitative automata. These automata
contain finitely many states and rational-valued transition weights, and their
common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum
map infinite words into the totallyordered domain of real numbers. In this automata-theoretic
setting, we establish a connection between quantitative safety and topological
continuity and provide an alternative characterization of quantitative safety
and liveness in terms of their boolean counterparts. For all common value functions,
we show how the safety closure of a quantitative automaton can be constructed
in PTime, and we provide PSpace-complete checks of whether a given quantitative
automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata,
for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf,
and LimSup automata, we give PTime decompositions into safe and live automata.
These decompositions enable the separation of techniques for safety and liveness
verification for quantitative specifications.
acknowledgement: We thank Christof Löding for pointing us to some results on PSpace-hardess
of universality problems and the anonymous reviewers for their helpful comments.
This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science
Foundation grant 2410/22.
alternative_title:
- LIPIcs
article_number: '17'
article_processing_charge: No
arxiv: 1
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative
automata. In: 34th International Conference on Concurrency Theory. Vol
279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17'
apa: 'Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023).
Safety and liveness of quantitative automata. In 34th International Conference
on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17'
chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac.
“Safety and Liveness of Quantitative Automata.” In 34th International Conference
on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.
ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness
of quantitative automata,” in 34th International Conference on Concurrency
Theory, Antwerp, Belgium, 2023, vol. 279.
ista: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness
of quantitative automata. 34th International Conference on Concurrency Theory.
CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.'
mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th
International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17.
short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-09-23
location: Antwerp, Belgium
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2023-09-18
date_created: 2023-07-14T10:00:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-10-09T07:14:03Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2023.17
ec_funded: 1
external_id:
arxiv:
- '2307.06016'
file:
- access_level: open_access
checksum: d40e57a04448ea5c77d7e1cfb9590a81
content_type: application/pdf
creator: esarac
date_created: 2023-07-14T12:03:48Z
date_updated: 2023-07-14T12:03:48Z
file_id: '13224'
file_name: CONCUR23.pdf
file_size: 755529
relation: main_file
success: 1
file_date_updated: 2023-07-14T12:03:48Z
has_accepted_license: '1'
intvolume: ' 279'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 34th International Conference on Concurrency Theory
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772990'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: Safety and liveness of quantitative automata
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: 279
year: '2023'
...
---
_id: '13262'
abstract:
- lang: eng
text: 'Determining the degree of inherent parallelism in classical sequential algorithms
and leveraging it for fast parallel execution is a key topic in parallel computing,
and detailed analyses are known for a wide range of classical algorithms. In this
paper, we perform the first such analysis for the fundamental Union-Find problem,
in which we are given a graph as a sequence of edges, and must maintain its connectivity
structure under edge additions. We prove that classic sequential algorithms for
this problem are well-parallelizable under reasonable assumptions, addressing
a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential
argument that, under uniform random edge ordering, parallel union-find operations
are unlikely to interfere: T concurrent threads processing the graph in parallel
will encounter memory contention O(T2 · log |V| · log |E|) times in expectation,
where |E| and |V| are the number of edges and nodes in the graph, respectively.
We leverage this result to design a new parallel Union-Find algorithm that is
both internally deterministic, i.e., its results are guaranteed to match those
of a sequential execution, but also work-efficient and scalable, as long as the
number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε
> 0, which holds for most large real-world graphs. We present lower bounds which
show that our analysis is close to optimal, and experimental results suggesting
that the performance cost of internal determinism is limited.'
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Diba
full_name: Hashemi, Diba
id: ed9595ea-2f8f-11ee-ba95-d2b546540783
last_name: Hashemi
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
- 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: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic
parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism
in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271.
doi:10.1145/3558481.3591082'
apa: 'Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient
and internally-deterministic parallel Union-Find. In Proceedings of the 35th
ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271).
Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082'
chicago: Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh.
“Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings
of the 35th ACM Symposium on Parallelism in Algorithms and Architectures,
261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.
ieee: A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient
and internally-deterministic parallel Union-Find,” in Proceedings of the 35th
ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL,
United States, 2023, pp. 261–271.
ista: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient
and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM
Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism
in Algorithms and Architectures, 261–271.'
mla: Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic
Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2023,
pp. 261–71, doi:10.1145/3558481.3591082.
short: A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association
for Computing Machinery, 2023, pp. 261–271.
conference:
end_date: 2023-06-19
location: Orlando, FL, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2023-06-17
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-17T00:00:00Z
date_updated: 2023-07-31T10:54:32Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1145/3558481.3591082
external_id:
arxiv:
- '2304.09331'
file:
- access_level: open_access
checksum: 72e312aabf0c5248c99b5cd3a88e4c88
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T10:53:08Z
date_updated: 2023-07-31T10:53:08Z
file_id: '13334'
file_name: 2023_SPAA_Fedorov.pdf
file_size: 2087937
relation: main_file
success: 1
file_date_updated: 2023-07-31T10:53:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 261-271
publication: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and
Architectures
publication_identifier:
isbn:
- '9781450395458'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Provably-efficient and internally-deterministic parallel Union-Find
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
year: '2023'
...
---
_id: '13274'
abstract:
- lang: eng
text: Viscous flows through pipes and channels are steady and ordered until, with
increasing velocity, the laminar motion catastrophically breaks down and gives
way to turbulence. How this apparently discontinuous change from low- to high-dimensional
motion can be rationalized within the framework of the Navier-Stokes equations
is not well understood. Exploiting geometrical properties of transitional channel
flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible
and identify the complete path that reversibly links fully turbulent motion to
an invariant solution. This precursor of turbulence destabilizes rapidly with
Re, and the accompanying explosive increase in attractor dimension effectively
marks the transition between deterministic and de facto stochastic dynamics.
acknowledgement: We thank Baofang Song as well as the developers of Channelflow for
sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful
discussions. This work was supported by a grant from the Simons Foundation (662960,
B. H.).
article_number: '034002'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Yohann
full_name: Duguet, Yohann
last_name: Duguet
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence
to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002
apa: Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023).
Direct path from turbulence to time-periodic solutions. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/physrevlett.131.034002
chicago: Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur,
and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical
Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.
ieee: C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct
path from turbulence to time-periodic solutions,” Physical Review Letters,
vol. 131, no. 3. American Physical Society, 2023.
ista: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from
turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.
mla: Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic
Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American
Physical Society, 2023, doi:10.1103/physrevlett.131.034002.
short: C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review
Letters 131 (2023).
date_created: 2023-07-24T09:43:59Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2023-12-13T11:40:19Z
day: '21'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/physrevlett.131.034002
external_id:
arxiv:
- '2306.05098'
isi:
- '001052929900004'
intvolume: ' 131'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.05098
month: '07'
oa: 1
oa_version: Preprint
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: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Direct path from turbulence to time-periodic solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '13286'
abstract:
- lang: eng
text: Semiconductor-superconductor hybrid systems are the harbour of many intriguing
mesoscopic phenomena. This material combination leads to spatial variations of
the superconducting properties, which gives rise to Andreev bound states (ABSs).
Some of these states might exhibit remarkable properties that render them highly
desirable for topological quantum computing. The most prominent and hunted of
such states are Majorana zero modes (MZMs), quasiparticles equals to their own
quasiparticles that they follow non-abelian statistics. In this thesis, we first
introduce the general framework of such hybrid systems and, then, we unveil a
series of mesoscopic phenomena that we discovered. Firstly, we show tunneling
spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot
states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures.
Then, we introduce a novel protocol which allowed the integration of tunneling
spectroscopy with Coulomb spectroscopy within the same device. Employing this
approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally
confined states reveal charge transport phenomenology similar to the one expected
for MZMs. These findings shed light on the intricate interplay between superconductivity
and quantum confinement, which brought us to explore another material platform,
i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce
superconductivity in such system, we showed how to engineer the proximity effect
and we revealed a superconducting hard gap. Finally, we created a superconducting
radio frequency driven ideal diode and a generator of non-sinusoidal current-phase
relations. Our results open the path for the exploration of protected superconducting
qubits and more complex hybrid devices in planar Germanium, like Kitaev chains
and hybrid qubit devices.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: 'Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286'
apa: 'Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286'
chicago: 'Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.'
ieee: 'M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,”
Institute of Science and Technology Austria, 2023.'
ista: 'Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria.'
mla: 'Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.'
short: 'M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium,
Institute of Science and Technology Austria, 2023.'
date_created: 2023-07-24T14:10:45Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2024-02-21T12:35:34Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:13286
ec_funded: 1
file:
- access_level: closed
checksum: 666ee31c7eade89679806287c062fa14
content_type: application/x-zip-compressed
creator: mvalenti
date_created: 2023-08-11T09:27:39Z
date_updated: 2023-08-11T10:01:34Z
file_id: '14033'
file_name: PhD_thesis_Valentini_final.zip
file_size: 56121429
relation: source_file
- access_level: open_access
checksum: 0992f2ebef152dee8e70055350ebbb55
content_type: application/pdf
creator: mvalenti
date_created: 2023-08-11T14:39:17Z
date_updated: 2023-08-11T14:39:17Z
file_id: '14035'
file_name: PhD_thesis_Valentini_final_validated.pdf
file_size: 38199711
relation: main_file
file_date_updated: 2023-08-11T14:39:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '184'
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: Conventional and unconventional topological superconductors
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13312'
relation: part_of_dissertation
status: public
- id: '12118'
relation: part_of_dissertation
status: public
- id: '8910'
relation: part_of_dissertation
status: public
- id: '12522'
relation: research_data
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: 'Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium'
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: '13292'
abstract:
- lang: eng
text: The operator precedence languages (OPLs) represent the largest known subclass
of the context-free languages which enjoys all desirable closure and decidability
properties. This includes the decidability of language inclusion, which is the
ultimate verification problem. Operator precedence grammars, automata, and logics
have been investigated and used, for example, to verify programs with arithmetic
expressions and exceptions (both of which are deterministic pushdown but lie outside
the scope of the visibly pushdown languages). In this paper, we complete the picture
and give, for the first time, an algebraic characterization of the class of OPLs
in the form of a syntactic congruence that has finitely many equivalence classes
exactly for the operator precedence languages. This is a generalization of the
celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of
the consequences, we show that universality and language inclusion for nondeterministic
operator precedence automata can be solved by an antichain algorithm. Antichain
algorithms avoid determinization and complementation through an explicit subset
construction, by leveraging a quasi-order on words, which allows the pruning of
the search space for counterexample words without sacrificing completeness. Antichain
algorithms can be implemented symbolically, and these implementations are today
the best-performing algorithms in practice for the inclusion of finite automata.
We give a generic construction of the quasi-order needed for antichain algorithms
from a finite syntactic congruence. This yields the first antichain algorithm
for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem
for OPLs in exponential time.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe
thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful
comments.\r\n"
alternative_title:
- LIPIcs
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Pavol
full_name: Kebis, Pavol
last_name: Kebis
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator
precedence languages. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129'
apa: 'Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023).
Regular methods for operator precedence languages. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129'
chicago: Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E
Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International
Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.
ieee: T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods
for operator precedence languages,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.
ista: 'Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for
operator precedence languages. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: International Colloquium on Automata, Languages, and Programming,
LIPIcs, vol. 261, 129:1--129:20.'
mla: Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.”
50th International Colloquium on Automata, Languages, and Programming,
vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20,
doi:10.4230/LIPIcs.ICALP.2023.129.
short: T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International
Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, p. 129:1--129:20.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-07-24T15:11:41Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2023-07-31T08:38:38Z
day: '05'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.4230/LIPIcs.ICALP.2023.129
ec_funded: 1
external_id:
arxiv:
- '2305.03447'
file:
- access_level: open_access
checksum: 5d4c8932ef3450615a53b9bb15d92eb2
content_type: application/pdf
creator: esarac
date_created: 2023-07-24T15:11:05Z
date_updated: 2023-07-24T15:11:05Z
file_id: '13293'
file_name: icalp23.pdf
file_size: 859379
relation: main_file
success: 1
file_date_updated: 2023-07-24T15:11:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 129:1--129:20
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772785'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: Regular methods for operator precedence languages
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '13310'
abstract:
- lang: eng
text: Machine-learned systems are in widespread use for making decisions about humans,
and it is important that they are fair, i.e., not biased against individuals based
on sensitive attributes. We present runtime verification of algorithmic fairness
for systems whose models are unknown, but are assumed to have a Markov chain structure.
We introduce a specification language that can model many common algorithmic fairness
properties, such as demographic parity, equal opportunity, and social burden.
We build monitors that observe a long sequence of events as generated by a given
system, and output, after each observation, a quantitative estimate of how fair
or biased the system was on that run until that point in time. The estimate is
proven to be correct modulo a variable error bound and a given confidence level,
where the error bound gets tighter as the observed sequence gets longer. Our monitors
are of two types, and use, respectively, frequentist and Bayesian statistical
inference techniques. While the frequentist monitors compute estimates that are
objectively correct with respect to the ground truth, the Bayesian monitors compute
estimates that are correct subject to a given prior belief about the system’s
model. Using a prototype implementation, we show how we can monitor if a bank
is fair in giving loans to applicants from different social backgrounds, and if
a college is fair in admitting students while maintaining a reasonable financial
burden on the society. Although they exhibit different theoretical complexities
in certain cases, in our experiments, both frequentist and Bayesian monitors took
less than a millisecond to update their verdicts after each observation.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG101020093.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Mahyar
full_name: Karimi, Mahyar
id: f1dedef5-2f78-11ee-989a-c4c97bccf506
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness.
In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382.
doi:10.1007/978-3-031-37703-7_17'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring
algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382).
Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17'
chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.
ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic
fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965,
pp. 358–382.
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic
fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13965, 358–382.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer
Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.
short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 358–382.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-07-25T18:32:40Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2023-09-05T15:14:00Z
day: '18'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-37703-7_17
ec_funded: 1
external_id:
arxiv:
- '2305.15979'
file:
- access_level: open_access
checksum: ccaf94bf7d658ba012c016e11869b54c
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:11:20Z
date_updated: 2023-07-31T08:11:20Z
file_id: '13327'
file_name: 2023_LNCS_CAV_HenzingerT.pdf
file_size: 647760
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:11:20Z
has_accepted_license: '1'
intvolume: ' 13965'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 358–382
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377037'
eissn:
- 1611-3349
isbn:
- '9783031377020'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Monitoring algorithmic fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13965
year: '2023'
...
---
_id: '13314'
abstract:
- lang: eng
text: The emergence of large-scale order in self-organized systems relies on local
interactions between individual components. During bacterial cell division, FtsZ—a
prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling
filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments
can form dynamic chiral assemblies. However, how the active and passive properties
of individual filaments relate to these large-scale self-organized structures
remains poorly understood. Here we connect single-filament properties with the
mesoscopic scale by combining minimal active matter simulations and biochemical
reconstitution experiments. We show that the density and flexibility of active
chiral filaments define their global order. At intermediate densities, curved,
flexible filaments organize into chiral rings and polar bands. An effectively
nematic organization dominates for high densities and for straight, mutant filaments
with increased rigidity. Our predicted phase diagram quantitatively captures these
features, demonstrating how the flexibility, density and chirality of the active
filaments affect their collective behaviour. Our findings shed light on the fundamental
properties of active chiral matter and explain how treadmilling FtsZ filaments
organize during bacterial cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'This work was supported by the European Research Council through
grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607
to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM
collaborative research program. Z.D. has received funding from Doctoral Programme
of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan
Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria),
Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments
on the manuscript. We are also thankful for the support by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Imaging and Optics
Facility (IOF) and the Lab Support Facility (LSF).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Batirtze
full_name: Prats Mateu, Batirtze
id: 299FE892-F248-11E8-B48F-1D18A9856A87
last_name: Prats Mateu
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Keesiang
full_name: Lim, Keesiang
last_name: Lim
- first_name: Dörte
full_name: Brandis, Dörte
id: 21d64d35-f128-11eb-9611-b8bcca7a12fd
last_name: Brandis
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Richard W.
full_name: Wong, Richard W.
last_name: Wong
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible
active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w
apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P.,
… Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature
Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w
chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte
Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of
Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.
ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,”
Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.
ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG,
Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible
active filaments. Nature Physics. 19, 1916–1926.
mla: Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.”
Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.
short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G.
Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023)
1916–1926.
date_created: 2023-07-27T14:44:45Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:19:08Z
day: '01'
ddc:
- '530'
department:
- _id: JoDa
- _id: EdHa
- _id: MaLo
- _id: GradSch
doi: 10.1038/s41567-023-02218-w
ec_funded: 1
external_id:
pmid:
- '38075437'
file:
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checksum: bc7673ca07d37309013a86166577b2f7
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creator: dernst
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file_name: 2023_NaturePhysics_Dunajova.pdf
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success: 1
file_date_updated: 2024-01-30T14:28:30Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1916-1926
pmid: 1
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: 34d75525-11ca-11ed-8bc3-89b6307fee9d
grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13116'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Chiral and nematic phases of flexible active filaments
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: '13331'
abstract:
- lang: eng
text: "The extension of extremal combinatorics to the setting of exterior algebra
is a work\r\nin progress that gained attention recently. In this thesis, we study
the combinatorial structure of exterior algebra by introducing a dictionary that
translates the notions from the set systems into the framework of exterior algebra.
We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner
theorem to the setting of exterior algebra in the simplest non-trivial case of
two-forms.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Seyda
full_name: Köse, Seyda
id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb
last_name: Köse
citation:
ama: Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331
apa: Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13331
chicago: Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science
and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.
ieee: S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology
Austria, 2023.
ista: Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and
Technology Austria.
mla: Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science
and Technology Austria, 2023, doi:10.15479/at:ista:13331.
short: S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-07-31T10:20:55Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2023-10-04T11:54:56Z
day: '31'
ddc:
- '510'
- '516'
degree_awarded: MS
department:
- _id: GradSch
- _id: UlWa
doi: 10.15479/at:ista:13331
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checksum: 96ee518d796d02af71395622c45de03c
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date_created: 2023-07-31T10:16:32Z
date_updated: 2023-07-31T10:16:32Z
file_id: '13333'
file_name: Exterior Algebra and Combinatorics.zip
file_size: 28684
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creator: skoese
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file_id: '13480'
file_name: thesis-pdfa.pdf
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- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12680'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Exterior algebra and combinatorics
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13984'
abstract:
- lang: eng
text: "Social insects fight disease using their individual immune systems and the
cooperative\r\nsanitary behaviors of colony members. These social defenses are
well explored against\r\nexternally-infecting pathogens, but little is known about
defense strategies against\r\ninternally-infecting pathogens, such as viruses.
Viruses are ubiquitous and in the last decades\r\nit has become evident that also
many ant species harbor viruses. We present one of the first\r\nstudies addressing
transmission dynamics and collective disease defenses against viruses in\r\nants
on a mechanistic level. I successfully established an experimental ant host –
viral\r\npathogen system as a model for the defense strategies used by social
insects against internal\r\npathogen infections, as outlined in the third chapter.
In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves
and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis
virus). We chose microinjections of virus directly into the ants’\r\nhemolymph
because it allowed us to use a defined exposure dose. Here we show that this is
a\r\ngood model system, as the virus is replicating and thus infecting the host.
The ants mount a\r\nclear individual immune response against the viral infection,
which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against
the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this
immune response is consistent with the timeline\r\nof viral replication that starts
already within two days post injection. The disease manifests in\r\ndecreased
survival over a course of two to three weeks.\r\nRegarding group living, we find
that infected ants show a strong individual immune response,\r\nbut that their
course of disease is little affected by nestmate presence, as described in chapter\r\nfour.
Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates,
however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed
that 94 % of the nestmates contract active virus within four days of social contact
to\r\nan infected individual. Virus is transmitted in low doses, thus not causing
disease\r\ntransmission within the colony. While virus can be transmitted during
short direct contacts,\r\nwe also assume transmission from deceased ants and show
that the nestmates’ immune\r\nsystem gets activated after contracting a low viral
dose. We find considerable potential for\r\nindirect transmission via the nest
space. Virus is shed to the nest, where it stays viable for one\r\nweek and is
also picked up by other ants. Apart from that, we want to underline the potential\r\nof
ant poison as antiviral agent. We determined that ant poison successfully inactivates
CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize
the nest space.\r\nOn the other hand, local application of ant poison by oral
poison uptake, which is part of the\r\nants prophylactic behavioral repertoire,
probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize
that oral poison uptake might be the reason why we did\r\nnot find viable virus
in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data
on potential social immunization. However,\r\nour experiments do not confirm an
actual survival benefit for the nestmates upon pathogen\r\nchallenge under the
given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility
for nestmate immunization, but rather emphasize that considering different\r\nexperimental
timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn
conclusion, we find that prophylactic individual behaviors, such as oral poison
uptake,\r\nmight play a role in preventing viral disease transmission. Compared
to colony defense\r\nagainst external pathogens, internal pathogen infections
require a stronger component of\r\nindividual physiological immunity than behavioral
social immunity, yet could still lead to\r\ncollective protection."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anna
full_name: Franschitz, Anna
id: 480826C8-F248-11E8-B48F-1D18A9856A87
last_name: Franschitz
citation:
ama: Franschitz A. Individual and social immunity against viral infections in ants.
2023. doi:10.15479/at:ista:13984
apa: Franschitz, A. (2023). Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984
chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections
in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.
ieee: A. Franschitz, “Individual and social immunity against viral infections in
ants,” Institute of Science and Technology Austria, 2023.
ista: Franschitz A. 2023. Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria.
mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections
in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.
short: A. Franschitz, Individual and Social Immunity against Viral Infections in
Ants, Institute of Science and Technology Austria, 2023.
date_created: 2023-08-08T15:33:29Z
date_published: 2023-08-08T00:00:00Z
date_updated: 2024-03-01T15:25:17Z
day: '08'
ddc:
- '570'
- '577'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/at:ista:13984
file:
- access_level: closed
checksum: 27220243d5d51c3b0d7d61c0879d7a0c
content_type: application/pdf
creator: afransch
date_created: 2023-08-08T18:01:28Z
date_updated: 2024-03-01T08:51:42Z
embargo: 2024-08-08
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file_id: '13986'
file_name: Thesis_AnnaFranschitz_202308.pdf
file_size: 10797612
relation: main_file
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: afransch
date_created: 2023-08-08T18:02:25Z
date_updated: 2023-08-09T07:25:27Z
file_id: '13987'
file_name: Thesis_AnnaFranschitz_202308.docx
file_size: 2619085
relation: source_file
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checksum: 8b991ecc2d59d045cc3cf0d676785ec7
content_type: application/pdf
creator: cchlebak
date_created: 2024-03-01T08:37:15Z
date_updated: 2024-03-01T12:13:29Z
description: Minor modifications and clarifications - Feb 2024
embargo: 2024-08-08
embargo_to: open_access
file_id: '15042'
file_name: Addendum_AnnaFranschitz202402.pdf
file_size: 85956
relation: erratum
title: Addendum
- access_level: closed
checksum: 66745aa01f960f17472c024875c049ed
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2024-03-01T08:39:20Z
date_updated: 2024-03-01T08:51:42Z
file_id: '15043'
file_name: Addendum_AnnaFranschitz202402.docx
file_size: 11818
relation: source_file
title: Addendum - source file
- access_level: closed
checksum: 55c876b73d49db15228a7f571592ec77
content_type: application/pdf
creator: cchlebak
date_created: 2024-03-01T08:56:06Z
date_updated: 2024-03-01T12:58:14Z
description: For printing purposes
file_id: '15044'
file_name: Print_Version_Franschitz_Anna_Thesis.pdf
file_size: 10416761
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title: Print Version
file_date_updated: 2024-03-01T12:58:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: '89'
publication_identifier:
isbn:
- 978-3-99078-034-3
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Individual and social immunity against viral infections in ants
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_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
file_id: '14899'
file_name: 2023_NaturePhysics_Mukhopadhyay.pdf
file_size: 1977706
relation: main_file
success: 1
file_date_updated: 2024-01-29T11:25:38Z
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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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
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success: 1
file_date_updated: 2024-01-30T12:48:24Z
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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
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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:
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department:
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- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
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checksum: c346016393123a0a2338ad4d976f61bc
content_type: application/pdf
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oa: 1
oa_version: Published Version
page: 156-169
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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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:
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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: '12349'
abstract:
- lang: eng
text: Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types.
acknowledged_ssus:
- _id: ScienComp
- _id: PreCl
- _id: LifeSc
- _id: Bio
acknowledgement: We thank Hiroki Asari for sharing the dataset of naturalistic images,
Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative
work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings.
We also thank Gasper Tkacik and members of the Neuroethology group for their comments
on the manuscript. This research was supported by the Scientific Service Units of
IST Austria through resources provided by Scientific Computing, the Preclinical
Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work
was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385
(DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers
Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European
Research Council Starting Grant 756502 (MJ).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Divyansh
full_name: Gupta, Divyansh
id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
orcid: 0000-0001-7400-6665
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Jan
full_name: Svaton, Jan
id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2
last_name: Svaton
orcid: 0000-0002-6198-2939
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature
Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0
apa: Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &
Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization
of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0
chicago: Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan
Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide
Organization of Receptive Fields.” Nature Neuroscience. Springer Nature,
2023. https://doi.org/10.1038/s41593-023-01280-0.
ieee: D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A.
Jösch, “Panoramic visual statistics shape retina-wide organization of receptive
fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.
ista: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience.
26, 606–614.
mla: Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization
of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023,
pp. 606–14, doi:10.1038/s41593-023-01280-0.
short: D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch,
Nature Neuroscience 26 (2023) 606–614.
date_created: 2023-01-23T14:14:19Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-10-04T11:41:05Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: MaJö
doi: 10.1038/s41593-023-01280-0
ec_funded: 1
external_id:
isi:
- '000955258300002'
pmid:
- '36959418'
file:
- access_level: open_access
checksum: a33d91e398e548f34003170e10988368
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T11:40:51Z
date_updated: 2023-10-04T11:40:51Z
file_id: '14395'
file_name: 2023_NatureNeuroscience_Gupta.pdf
file_size: 6144866
relation: main_file
success: 1
file_date_updated: 2023-10-04T11:40:51Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 606-614
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12370'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Panoramic visual statistics shape retina-wide organization of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...