---
_id: '12839'
abstract:
- lang: eng
text: Universal nonequilibrium properties of isolated quantum systems are typically
probed by studying transport of conserved quantities, such as charge or spin,
while transport of energy has received considerably less attention. Here, we study
infinite-temperature energy transport in the kinetically constrained PXP model
describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations,
including exact diagonalization and time-evolving block decimation methods, reveal
the existence of two distinct transport regimes. At moderate times, the energy-energy
correlation function displays periodic oscillations due to families of eigenstates
forming different su(2) representations hidden within the spectrum. These families
of eigenstates generalize the quantum many-body scarred states found in previous
works and leave an imprint on the infinite-temperature energy transport. At later
times, we observe a long-lived superdiffusive transport regime that we attribute
to the proximity of a nearby integrable point. While generic strong deformations
of the PXP model indeed restore diffusive transport, adding a strong chemical
potential intriguingly gives rise to a well-converged superdiffusive exponent
z≈3/2. Our results suggest constrained models to be potential hosts of novel transport
regimes and call for developing an analytic understanding of their energy transport.
acknowledgement: "We would like to thank Alexios Michailidis, Sarang Gopalakrishnan,
and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support
by the European Research Council under the European Union’s Horizon 2020 research
and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge
support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership
Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research
data: This publication is theoretical work that does not require supporting research
data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International
Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for
awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations
were performed. The TEBD\r\nsimulations were performed using the ITENSOR library
[54]."
article_number: '011033'
article_processing_charge: No
article_type: original
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Jean Yves
full_name: Desaules, Jean Yves
last_name: Desaules
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033
apa: Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive
energy transport in kinetically constrained models. Physical Review X.
American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033
chicago: Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić.
“Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical
Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.
ieee: M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy
transport in kinetically constrained models,” Physical Review X, vol. 13,
no. 1. American Physical Society, 2023.
ista: Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport
in kinetically constrained models. Physical Review X. 13(1), 011033.
mla: Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained
Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society,
2023, doi:10.1103/PhysRevX.13.011033.
short: M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).
date_created: 2023-04-16T22:01:09Z
date_published: 2023-03-07T00:00:00Z
date_updated: 2023-08-01T14:11:28Z
day: '07'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevX.13.011033
ec_funded: 1
external_id:
isi:
- '000957625700001'
file:
- access_level: open_access
checksum: ee060cea609af79bba7af74b1ce28078
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T08:36:53Z
date_updated: 2023-04-17T08:36:53Z
file_id: '12845'
file_name: 2023_PhysReviewX_Ljubotina.pdf
file_size: 1958523
relation: main_file
success: 1
file_date_updated: 2023-04-17T08:36:53Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superdiffusive energy transport in kinetically constrained models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '12846'
abstract:
- lang: eng
text: We present a formula for the signed area of a spherical polygon via prequantization.
In contrast to the traditional formula based on the Gauss-Bonnet theorem that
requires measuring angles, the new formula mimics Green's theorem and is applicable
to a wider range of degenerate spherical curves and polygons.
acknowledgement: The authors acknowledge Chris Wojtan for his continuous support to
the present work through discussions and advice. The second author thanks Anna Sisak
for a fruitful discussion on prequantum bundles. This project was funded in part
by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).
article_number: '2303.14555'
article_processing_charge: No
arxiv: 1
author:
- first_name: Albert
full_name: Chern, Albert
last_name: Chern
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
citation:
ama: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv. doi:10.48550/arXiv.2303.14555
apa: Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via
prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555
chicago: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons
via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.
ieee: A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,”
arXiv. .
ista: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv, 2303.14555.
mla: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via
Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.
short: A. Chern, S. Ishida, ArXiv (n.d.).
date_created: 2023-04-18T19:16:06Z
date_published: 2023-03-25T00:00:00Z
date_updated: 2023-04-25T06:51:21Z
day: '25'
department:
- _id: GradSch
- _id: ChWo
doi: 10.48550/arXiv.2303.14555
external_id:
arxiv:
- '2303.14555'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2303.14555
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: arXiv
publication_status: submitted
status: public
title: Area formula for spherical polygons via prequantization
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12854'
abstract:
- lang: eng
text: "The main idea behind BUBAAK is to run multiple program analyses in parallel
and use runtime monitoring and enforcement to observe and control their progress
in real time. The analyses send information about (un)explored states of the program
and discovered invariants to a monitor. The monitor processes the received data
and can force an analysis to stop the search of certain program parts (which have
already been analyzed by other analyses), or to make it utilize a program invariant
found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange
between the monitor and the analyses was not yet completed, which is why BUBAAK
only ran several analyses in parallel, without any coordination. Still, BUBAAK
won the meta-category FalsificationOverall and placed very well in several other
(sub)-categories of the competition."
acknowledgement: This work was supported by the ERC-2020-AdG 10102009 grant.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers.
In: Tools and Algorithms for the Construction and Analysis of Systems.
Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of
program verifiers. In Tools and Algorithms for the Construction and Analysis
of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32'
chicago: 'Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of
Program Verifiers.” In Tools and Algorithms for the Construction and Analysis
of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.'
ieee: 'M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,”
in Tools and Algorithms for the Construction and Analysis of Systems, Paris,
France, 2023, vol. 13994, pp. 535–540.'
ista: 'Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers.
Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994,
535–540.'
mla: 'Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program
Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems,
vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.'
short: M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction
and Analysis of Systems, Springer Nature, 2023, pp. 535–540.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2023-04-22
date_created: 2023-04-20T08:22:53Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:02:43Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30820-8_32
ec_funded: 1
file:
- access_level: open_access
checksum: 120d2c2a38384058ad0630fdf8288312
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T06:58:36Z
date_updated: 2023-04-25T06:58:36Z
file_id: '12864'
file_name: 2023_LNCS_Chalupa.pdf
file_size: 16096413
relation: main_file
success: 1
file_date_updated: 2023-04-25T06:58:36Z
has_accepted_license: '1'
intvolume: ' 13994'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 535-540
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783031308208'
eissn:
- 1611-3349
isbn:
- '9783031308192'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Bubaak: Runtime monitoring of program verifiers'
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: 13994
year: '2023'
...
---
_id: '12856'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort
third-party monitoring. In: Fundamental Approaches to Software Engineering.
Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches
to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer
Nature. https://doi.org/10.1007/978-3-031-30826-0_15'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
“Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental
Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware
for best-effort third-party monitoring,” in Fundamental Approaches to Software
Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware
for best-effort third-party monitoring. Fundamental Approaches to Software Engineering.
FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.'
mla: 'Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.”
Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature,
2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.'
short: M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental
Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2023-04-22
date_created: 2023-04-20T08:29:42Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:19:07Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30826-0_15
ec_funded: 1
file:
- access_level: open_access
checksum: 17a7c8e08be609cf2408d37ea55e322c
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T07:16:36Z
date_updated: 2023-04-25T07:16:36Z
file_id: '12865'
file_name: 2023_LNCS_ChalupaM.pdf
file_size: 580828
relation: main_file
success: 1
file_date_updated: 2023-04-25T07:16:36Z
has_accepted_license: '1'
intvolume: ' 13991'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 260-281
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eisbn:
- '9783031308260'
eissn:
- 1611-3349
isbn:
- '9783031308253'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12407'
relation: earlier_version
status: public
status: public
title: 'Vamos: Middleware for best-effort third-party monitoring'
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: 13991
year: '2023'
...
---
_id: '12859'
abstract:
- lang: eng
text: 'Machine learning models are vulnerable to adversarial perturbations, and
a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through
the lens of over-parameterization: interpolating smoothly the data requires significantly
more parameters than simply memorizing it. However, this "universal" law provides
only a necessary condition for robustness, and it is unable to discriminate between
models. In this paper, we address these gaps by focusing on empirical risk minimization
in two prototypical settings, namely, random features and the neural tangent kernel
(NTK). We prove that, for random features, the model is not robust for any degree
of over-parameterization, even when the necessary condition coming from the universal
law of robustness is satisfied. In contrast, for even activations, the NTK model
meets the universal lower bound, and it is robust as soon as the necessary condition
on over-parameterization is fulfilled. This also addresses a conjecture in prior
work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel
of the model from an "interaction matrix", which describes the interaction with
the test data and captures the effect of the activation. Our theoretical results
are corroborated by numerical evidence on both synthetic and standard datasets
(MNIST, CIFAR-10).'
acknowledgement: "Simone Bombari and Marco Mondelli were partially supported by the
2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for
helpful discussions.\r\n"
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Shayan
full_name: Kiyani, Shayan
id: f5a2b424-e339-11ed-8435-ff3b4fe70cf8
last_name: Kiyani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper
laws for random features and neural tangent kernels. In: Proceedings of the
40th International Conference on Machine Learning. Vol 202. ML Research Press;
2023:2738-2776.'
apa: 'Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law
of robustness: Sharper laws for random features and neural tangent kernels. In
Proceedings of the 40th International Conference on Machine Learning (Vol.
202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.'
chicago: 'Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal
Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.”
In Proceedings of the 40th International Conference on Machine Learning,
202:2738–76. ML Research Press, 2023.'
ieee: 'S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, HI, United
States, 2023, vol. 202, pp. 2738–2776.'
ista: 'Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels. Proceedings of the
40th International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 202, 2738–2776.'
mla: 'Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws
for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.'
short: S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International
Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.
conference:
end_date: 2023-07-29
location: Honolulu, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-04-23T16:11:03Z
date_published: 2023-10-27T00:00:00Z
date_updated: 2024-09-10T13:03:19Z
day: '27'
department:
- _id: GradSch
- _id: MaMo
external_id:
arxiv:
- '2302.01629'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2302.01629
month: '10'
oa: 1
oa_version: Preprint
page: 2738-2776
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 40th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/simone-bombari/beyond-universal-robustness
status: public
title: 'Beyond the universal law of robustness: Sharper laws for random features and
neural tangent kernels'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '12861'
abstract:
- lang: eng
text: The field of indirect reciprocity investigates how social norms can foster
cooperation when individuals continuously monitor and assess each other’s social
interactions. By adhering to certain social norms, cooperating individuals can
improve their reputation and, in turn, receive benefits from others. Eight social
norms, known as the “leading eight," have been shown to effectively promote the
evolution of cooperation as long as information is public and reliable. These
norms categorize group members as either ’good’ or ’bad’. In this study, we examine
a scenario where individuals instead assign nuanced reputation scores to each
other, and only cooperate with those whose reputation exceeds a certain threshold.
We find both analytically and through simulations that such quantitative assessments
are error-correcting, thus facilitating cooperation in situations where information
is private and unreliable. Moreover, our results identify four specific norms
that are robust to such conditions, and may be relevant for helping to sustain
cooperation in natural populations.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support
by the Stochastic Analysis and Application Research Center (SAARC) under National
Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally
thank Stefan Schmid for providing access to his lab infrastructure at the University
of Vienna for the purpose of collecting simulation data.'
article_number: '2086'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Farbod
full_name: Ekbatani, Farbod
last_name: Ekbatani
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize
indirect reciprocity under imperfect information. Nature Communications.
2023;14. doi:10.1038/s41467-023-37817-x
apa: Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative
assessment can stabilize indirect reciprocity under imperfect information. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x
chicago: Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee.
“Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.
ieee: L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment
can stabilize indirect reciprocity under imperfect information,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment
can stabilize indirect reciprocity under imperfect information. Nature Communications.
14, 2086.
mla: Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity
under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer
Nature, 2023, doi:10.1038/s41467-023-37817-x.
short: L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14
(2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2025-07-14T09:09:52Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-37817-x
ec_funded: 1
external_id:
isi:
- '001003644100020'
pmid:
- '37045828'
file:
- access_level: open_access
checksum: a4b3b7b36fbef068cabf4fb99501fef6
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T09:13:53Z
date_updated: 2023-04-25T09:13:53Z
file_id: '12868'
file_name: 2023_NatureComm_Schmid.pdf
file_size: 1786475
relation: main_file
success: 1
file_date_updated: 2023-04-25T09:13:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative assessment can stabilize indirect reciprocity under imperfect
information
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: 14
year: '2023'
...
---
_id: '12862'
abstract:
- lang: eng
text: Despite the considerable progress of in vivo neural recording techniques,
inferring the biophysical mechanisms underlying large scale coordination of brain
activity from neural data remains challenging. One obstacle is the difficulty
to link high dimensional functional connectivity measures to mechanistic models
of network activity. We address this issue by investigating spike-field coupling
(SFC) measurements, which quantify the synchronization between, on the one hand,
the action potentials produced by neurons, and on the other hand mesoscopic “field”
signals, reflecting subthreshold activities at possibly multiple recording sites.
As the number of recording sites gets large, the amount of pairwise SFC measurements
becomes overwhelmingly challenging to interpret. We develop Generalized Phase
Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate
SFC. GPLA describes the dominant coupling between field activity and neural ensembles
across space and frequencies. We show that GPLA features are biophysically interpretable
when used in conjunction with appropriate network models, such that we can identify
the influence of underlying circuit properties on these features. We demonstrate
the statistical benefits and interpretability of this approach in various computational
models and Utah array recordings. The results suggest that GPLA, used jointly
with biophysical modeling, can help uncover the contribution of recurrent microcircuits
to the spatio-temporal dynamics observed in multi-channel experimental recordings.
acknowledgement: "We thank Britni Crocker for help with preprocessing of the data
and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support;
Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll
authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal
Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe
Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from
the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02).
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript. "
article_number: e1010983
article_processing_charge: No
article_type: original
author:
- first_name: Shervin
full_name: Safavi, Shervin
last_name: Safavi
- first_name: Theofanis I.
full_name: Panagiotaropoulos, Theofanis I.
last_name: Panagiotaropoulos
- first_name: Vishal
full_name: Kapoor, Vishal
last_name: Kapoor
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
citation:
ama: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK,
Besserve M. Uncovering the organization of neural circuits with Generalized Phase
Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983
apa: Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F.,
Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural
circuits with Generalized Phase Locking Analysis. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983
chicago: Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F
Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization
of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational
Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.
ieee: S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N.
K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits
with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol.
19, no. 4. Public Library of Science, 2023.
ista: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis
NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized
Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.
mla: Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with
Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19,
no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.
short: S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K.
Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-01T14:15:16Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pcbi.1010983
external_id:
isi:
- '000962668700002'
file:
- access_level: open_access
checksum: edeb9d09f3e41ba7c0251308b9e372e7
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T08:59:18Z
date_updated: 2023-04-25T08:59:18Z
file_id: '12867'
file_name: 2023_PLoSCompBio_Safavi.pdf
file_size: 4737671
relation: main_file
success: 1
file_date_updated: 2023-04-25T08:59:18Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/shervinsafavi/gpla.git
scopus_import: '1'
status: public
title: Uncovering the organization of neural circuits with Generalized Phase Locking
Analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '12863'
abstract:
- lang: eng
text: In the present study, essential and nonessential metal content and biomarker
responses were investigated in the intestine of fish collected from the areas
polluted by mining. Our objective was to determine metal and biomarker levels
in tissue responsible for dietary intake, which is rarely studied in water pollution
research. The study was conducted in the Bregalnica River, reference location,
and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which
are directly influenced by the active mines Zletovo and Toranica, respectively.
Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman,
1928), using for the first time intestinal cytosol as a potentially toxic cell
fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic
metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo,
Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River
compared to the Bregalnica River in both seasons). The same trend was evident
for total proteins, biomarkers of general stress, and metallothioneins, biomarkers
of metal exposure, indicating cellular disturbances in the intestine, the primary
site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations
pointed to similar pathways and homeostasis of these metallothionein-binding metals.
Comparison with other indicator tissues showed that metal concentrations were
higher in the intestine of fish from mining-affected areas than in the liver and
gills. In general, these results indicated the importance of dietary metal pathways,
and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.
acknowledgement: 'The authors are grateful to Dr. Nevenka Mikac for the opportunity
to perform metal measurements on HR ICP-MS. This research was funded by the Ministry
of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721
and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian
bilateral projects: “The assessment of availability and effects of metals on fish
in the rivers under the impact of mining activities” and “Bacterial and parasitical
communities of chub as indicators of the status of environment exposed to mining
activities.”'
article_processing_charge: No
article_type: original
author:
- first_name: Vlatka
full_name: Filipović Marijić, Vlatka
last_name: Filipović Marijić
- first_name: Nesrete
full_name: Krasnici, Nesrete
id: cb5852d4-287f-11ed-baf0-bc1dd2d5c745
last_name: Krasnici
- first_name: Damir
full_name: Valić, Damir
last_name: Valić
- first_name: Damir
full_name: Kapetanović, Damir
last_name: Kapetanović
- first_name: Irena
full_name: Vardić Smrzlić, Irena
last_name: Vardić Smrzlić
- first_name: Maja
full_name: Jordanova, Maja
last_name: Jordanova
- first_name: Katerina
full_name: Rebok, Katerina
last_name: Rebok
- first_name: Sheriban
full_name: Ramani, Sheriban
last_name: Ramani
- first_name: Vasil
full_name: Kostov, Vasil
last_name: Kostov
- first_name: Rodne
full_name: Nastova, Rodne
last_name: Nastova
- first_name: Zrinka
full_name: Dragun, Zrinka
last_name: Dragun
citation:
ama: Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal
and biomarker responses in intestinal cytosol of freshwater fish. Environmental
Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2
apa: Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić,
I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish. Environmental Science and
Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2
chicago: Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović,
Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact
on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental
Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2.
ieee: V. Filipović Marijić et al., “Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish,” Environmental Science
and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023.
ista: Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I,
Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution
impact on metal and biomarker responses in intestinal cytosol of freshwater fish.
Environmental Science and Pollution Research. 30, 63510–63521.
mla: Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker
Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science
and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2.
short: V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić,
M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental
Science and Pollution Research 30 (2023) 63510–63521.
date_created: 2023-04-23T22:01:03Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T11:23:10Z
day: '01'
department:
- _id: LifeSc
doi: 10.1007/s11356-023-26844-2
external_id:
isi:
- '000970917900012'
pmid:
- '37055686'
intvolume: ' 30'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 63510-63521
pmid: 1
publication: Environmental Science and Pollution Research
publication_identifier:
eissn:
- 1614-7499
issn:
- 0944-1344
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pollution impact on metal and biomarker responses in intestinal cytosol of
freshwater fish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '12866'
abstract:
- lang: eng
text: "Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental
disorders. Extensive research has demonstrated shared pathological pathways, etiologies,
and phenotypes. Many risk factors for these disorders, like genetic mutations
and environmental pressures, are linked to changes in childhood brain development,
which is a critical period for their manifestation.\r\nDecades of research have
yielded many signatures for ASD and epilepsy, some shared and others unique or
opposing. The anatomical, physiological, and behavioral correlates of these disorders
are discussed in this chapter in the context of understanding shared pathological
pathways. We end with important takeaways on the presentation, prevention, intervention,
and policy changes for ASD and epilepsy. This chapter aims to explore the complexity
of these disorders, both in etiology and phenotypes, with the further goal of
appreciating the expanse of unknowns still to explore about the brain."
alternative_title:
- 'Vol. 1: Biological Development and Physical Health'
article_processing_charge: No
author:
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Chad
full_name: Beyer, Chad
last_name: Beyer
citation:
ama: 'Currin C, Beyer C. Altered childhood brain development in autism and epilepsy.
In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health.
1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1'
apa: Currin, C., & Beyer, C. (2023). Altered childhood brain development in
autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and
Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1
chicago: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development
in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health,
edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.
ieee: C. Currin and C. Beyer, “Altered childhood brain development in autism and
epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B.
Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.
ista: 'Currin C, Beyer C. 2023.Altered childhood brain development in autism and
epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological
Development and Physical Health, , 86–98.'
mla: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in
Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited
by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.
short: C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child
and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.
date_created: 2023-04-25T07:52:43Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-04-25T09:25:40Z
day: '01'
department:
- _id: TiVo
doi: 10.1016/b978-0-12-818872-9.00129-1
edition: '1'
editor:
- first_name: Bonnie
full_name: Halpern-Felsher, Bonnie
last_name: Halpern-Felsher
language:
- iso: eng
month: '02'
oa_version: None
page: 86-98
publication: Encyclopedia of Child and Adolescent Health
publication_identifier:
isbn:
- '9780128188736'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Altered childhood brain development in autism and epilepsy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12869'
abstract:
- lang: eng
text: 'We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately round cultures get a competitive advantage. We first analyse the
model with periodic boundary conditions, where we study how the model can end
up in a fixed state, i.e. freezes. Then we implement the model on the European
geography with mountains and rivers. We see how the model reproduces some qualitative
features of European culture formation, namely that rivers and mountains are more
frequently borders between cultures, mountainous regions tend to have higher cultural
diversity and the central European plain has less clear cultural borders. '
acknowledgement: 'FRK acknowledges support from the Villum Foundation for support
through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator
(Grant No. 25452) programs. '
article_processing_charge: No
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton
model of culture formation. 2023. doi:10.15479/AT:ISTA:12869'
apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic
cellular automaton model of culture formation. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:12869'
chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data
for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.'
ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular
automaton model of culture formation.” Institute of Science and Technology Austria,
2023.'
ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular
automaton model of culture formation, Institute of Science and Technology Austria,
10.15479/AT:ISTA:12869.'
mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for:
A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.'
short: F.R. Klausen, A.B. Lauritsen, (2023).
date_created: 2023-04-26T12:34:49Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-11-13T07:47:29Z
day: '26'
ddc:
- '000'
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/AT:ISTA:12869
file:
- access_level: open_access
checksum: 85ede12d38bb8d944022a8cba4d719f5
content_type: application/octet-stream
creator: alaurits
date_created: 2023-04-26T12:30:06Z
date_updated: 2023-04-26T12:30:06Z
file_id: '12870'
file_name: README.md
file_size: 4567
relation: main_file
success: 1
- access_level: open_access
checksum: 25bf79452ae895f9c8a20571a096b4c3
content_type: application/x-zip-compressed
creator: alaurits
date_created: 2023-04-26T12:27:34Z
date_updated: 2023-04-26T12:27:34Z
file_id: '12871'
file_name: simulations_era=10_flux_varied_europe.zip
file_size: 732586731
relation: main_file
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month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14505'
relation: used_in_publication
status: for_moderation
- id: '12890'
relation: used_in_publication
status: public
status: public
title: 'Research data for: A stochastic cellular automaton model of culture formation'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12876'
abstract:
- lang: eng
text: "Motivation: The problem of model inference is of fundamental importance to
systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally
attractive approach capable of handling large biological networks. The models
are typically inferred from experimental data. However, even with a substantial
amount of experimental data supported by some prior knowledge, existing inference
methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults:
We propose Boolean network sketches as a new formal instrument for the inference
of Boolean networks. A sketch integrates (typically partial) knowledge about the
network’s topology and the update logic (obtained through, e.g. a biological knowledge
base or a literature search), as well as further assumptions about the properties
of the network’s transitions (e.g. the form of its attractor landscape), and additional
restrictions on the model dynamics given by the measured experimental data. Our
new BNs inference algorithm starts with an ‘initial’ sketch, which is extended
by adding restrictions representing experimental data to a ‘data-informed’ sketch
and subsequently computes all BNs consistent with the data-informed sketch. Our
algorithm is based on a symbolic representation and coloured model-checking. Our
approach is unique in its ability to cover a broad spectrum of knowledge and efficiently
produce a compact representation of all inferred BNs. We evaluate the method on
a non-trivial collection of real-world and simulated data."
acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S];
and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was
partially supported by European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].
article_number: btad158
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Ondřej
full_name: Huvar, Ondřej
last_name: Huvar
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
citation:
ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 2023;39(4).
doi:10.1093/bioinformatics/btad158'
apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean
network sketches: A unifying framework for logical model inference. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158'
chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek.
“Boolean Network Sketches: A Unifying Framework for Logical Model Inference.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.'
ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network
sketches: A unifying framework for logical model inference,” Bioinformatics,
vol. 39, no. 4. Oxford Academic, 2023.'
ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.'
mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for
Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford
Academic, 2023, doi:10.1093/bioinformatics/btad158.'
short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).
date_created: 2023-04-30T22:01:05Z
date_published: 2023-04-03T00:00:00Z
date_updated: 2023-08-01T14:27:28Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad158
ec_funded: 1
external_id:
isi:
- '000976610800001'
pmid:
- '37004199'
file:
- access_level: open_access
checksum: 2cb90ddf781baefddf47eac4b54e2a03
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:39:04Z
date_updated: 2023-05-02T07:39:04Z
file_id: '12886'
file_name: 2023_Bioinformatics_Benes.pdf
file_size: 478740
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:39:04Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.7688740
scopus_import: '1'
status: public
title: 'Boolean network sketches: A unifying framework for logical model inference'
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: 39
year: '2023'
...
---
_id: '12877'
abstract:
- lang: eng
text: We consider billiards obtained by removing from the plane finitely many strictly
convex analytic obstacles satisfying the non-eclipse condition. The restriction
of the dynamics to the set of non-escaping orbits is conjugated to a subshift,
which provides a natural labeling of periodic orbits. We show that under suitable
symmetry and genericity assumptions, the Marked Length Spectrum determines the
geometry of the billiard table.
acknowledgement: 'J.D.S. and M.L. have been partially supported by the NSERC Discovery
grant, reference number 502617-2017. M.L. was also supported by the ERC project
692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally
symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR
JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012).
V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Martin
full_name: Leguil, Martin
last_name: Leguil
citation:
ama: De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic
chaotic billiards with axial symmetries. Inventiones Mathematicae. 2023;233:829-901.
doi:10.1007/s00222-023-01191-8
apa: De Simoi, J., Kaloshin, V., & Leguil, M. (2023). Marked Length Spectral
determination of analytic chaotic billiards with axial symmetries. Inventiones
Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-023-01191-8
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral
Determination of Analytic Chaotic Billiards with Axial Symmetries.” Inventiones
Mathematicae. Springer Nature, 2023. https://doi.org/10.1007/s00222-023-01191-8.
ieee: J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries,” Inventiones Mathematicae,
vol. 233. Springer Nature, pp. 829–901, 2023.
ista: De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae.
233, 829–901.
mla: De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic
Chaotic Billiards with Axial Symmetries.” Inventiones Mathematicae, vol.
233, Springer Nature, 2023, pp. 829–901, doi:10.1007/s00222-023-01191-8.
short: J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023)
829–901.
date_created: 2023-04-30T22:01:05Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-10-04T11:25:37Z
day: '01'
department:
- _id: VaKa
doi: 10.1007/s00222-023-01191-8
ec_funded: 1
external_id:
arxiv:
- '1905.00890'
isi:
- '000978887600001'
intvolume: ' 233'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.00890
month: '08'
oa: 1
oa_version: Preprint
page: 829-901
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Inventiones Mathematicae
publication_identifier:
eissn:
- 1432-1297
issn:
- 0020-9910
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Marked Length Spectral determination of analytic chaotic billiards with axial
symmetries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 233
year: '2023'
...
---
_id: '12878'
abstract:
- lang: eng
text: Salicylic acid (SA) plays important roles in different aspects of plant development,
including root growth, where auxin is also a major player by means of its asymmetric
distribution. However, the mechanism underlying the effect of SA on the development
of rice roots remains poorly understood. Here, we show that SA inhibits rice root
growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated
gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive
trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis
of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter
is at the center of a GRN involving the coat protein clathrin. The root growth
and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were
SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent
on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin
A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data
reveal that SA affects rice root growth through the convergence of transcriptional
and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and
clathrin-mediated trafficking as key components.
acknowledgement: The authors thank Professor Jianqiang Wu (Kunming Institute of Botany,
Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also
go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit
Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70
and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences)
for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania
State University) for provision of the rice line NahG. This work was supported by
grants from the National Natural Science Foundation of China (Grant Nos. 32260085,
31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects
of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major
Special Program for Scientific Research, Education Department of Yunnan Province
(Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden,
and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF
for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project
in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged
academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).
article_processing_charge: No
article_type: original
author:
- first_name: Lihui
full_name: Jiang, Lihui
last_name: Jiang
- first_name: Baolin
full_name: Yao, Baolin
last_name: Yao
- first_name: Xiaoyan
full_name: Zhang, Xiaoyan
last_name: Zhang
- first_name: Lixia
full_name: Wu, Lixia
last_name: Wu
- first_name: Qijing
full_name: Fu, Qijing
last_name: Fu
- first_name: Yiting
full_name: Zhao, Yiting
last_name: Zhao
- first_name: Yuxin
full_name: Cao, Yuxin
last_name: Cao
- first_name: Ruomeng
full_name: Zhu, Ruomeng
last_name: Zhu
- first_name: Xinqi
full_name: Lu, Xinqi
last_name: Lu
- first_name: Wuying
full_name: Huang, Wuying
last_name: Huang
- first_name: Jianping
full_name: Zhao, Jianping
last_name: Zhao
- first_name: Kuixiu
full_name: Li, Kuixiu
last_name: Li
- first_name: Shuanglu
full_name: Zhao, Shuanglu
last_name: Zhao
- first_name: Li
full_name: Han, Li
last_name: Han
- first_name: Xuan
full_name: Zhou, Xuan
last_name: Zhou
- first_name: Chongyu
full_name: Luo, Chongyu
last_name: Luo
- first_name: Haiyan
full_name: Zhu, Haiyan
last_name: Zhu
- first_name: Jing
full_name: Yang, Jing
last_name: Yang
- first_name: Huichuan
full_name: Huang, Huichuan
last_name: Huang
- first_name: Zhengge
full_name: Zhu, Zhengge
last_name: Zhu
- first_name: Xiahong
full_name: He, Xiahong
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhongkai
full_name: Zhang, Zhongkai
last_name: Zhang
- first_name: Changning
full_name: Liu, Changning
last_name: Liu
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
citation:
ama: Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein
trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal.
2023;115(1):155-174. doi:10.1111/tpj.16218
apa: Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic
acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin
to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218
chicago: Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao,
Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal.
Wiley, 2023. https://doi.org/10.1111/tpj.16218.
ieee: L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking
mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal,
vol. 115, no. 1. Wiley, pp. 155–174, 2023.
ista: Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W,
Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He
X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic
protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant
Journal. 115(1), 155–174.
mla: Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal,
vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218.
short: L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu,
W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H.
Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023)
155–174.
date_created: 2023-04-30T22:01:06Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-01T14:16:33Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.16218
external_id:
isi:
- '000971861400001'
pmid:
- '37025008 '
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 155-174
pmid: 1
publication: Plant Journal
publication_identifier:
eissn:
- 1365-313X
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t
and clathrin to affect root growth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 115
year: '2023'
...
---
_id: '12879'
abstract:
- lang: eng
text: Machine learning (ML) has been widely applied to chemical property prediction,
most prominently for the energies and forces in molecules and materials. The strong
interest in predicting energies in particular has led to a ‘local energy’-based
paradigm for modern atomistic ML models, which ensures size-extensivity and a
linear scaling of computational cost with system size. However, many electronic
properties (such as excitation energies or ionization energies) do not necessarily
scale linearly with system size and may even be spatially localized. Using size-extensive
models in these cases can lead to large errors. In this work, we explore different
strategies for learning intensive and localized properties, using HOMO energies
in organic molecules as a representative test case. In particular, we analyze
the pooling functions that atomistic neural networks use to predict molecular
properties, and suggest an orbital weighted average (OWA) approach that enables
the accurate prediction of orbital energies and locations.
acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is
grateful for the TUM graduate school finance support to visit Bingqing Cheng's group
in IST for two months. We also thankfully acknowledge computational resources provided
by the MPCDF Supercomputing Centre.
article_processing_charge: No
article_type: original
author:
- first_name: Ke
full_name: Chen, Ke
id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d
last_name: Chen
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
citation:
ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning
of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j
apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired
machine learning of localized intensive properties. Chemical Science. Royal
Society of Chemistry. https://doi.org/10.1039/d3sc00841j
chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes
T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.”
Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.
ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired
machine learning of localized intensive properties,” Chemical Science.
Royal Society of Chemistry, 2023.
ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine
learning of localized intensive properties. Chemical Science.
mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive
Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.
short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:18:10Z
day: '10'
ddc:
- '000'
- '540'
department:
- _id: BiCh
doi: 10.1039/d3sc00841j
external_id:
isi:
- '000971508100001'
file:
- access_level: open_access
checksum: 5eeec69a51e192dcd94b955d84423836
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:17:05Z
date_updated: 2023-05-02T07:17:05Z
file_id: '12883'
file_name: 2023_ChemialScience_Chen.pdf
file_size: 1515446
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:17:05Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics-inspired machine learning of localized intensive properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12880'
abstract:
- lang: eng
text: Peripheral heterochromatin positioning depends on nuclear envelope associated
proteins and repressive histone modifications. Here we show that overexpression
(OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin
into heterochromatic foci within the nucleoplasm. These changes represent a perturbation
of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent
from altering other heterochromatin anchors or histone post-translational modifications.
We further show that LmnB1 OE alters gene expression. These changes do not correlate
with different levels of H3K9me3, but a significant number of the misregulated
genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed
an enrichment of developmental processes amongst the upregulated genes. ~74% of
these genes were normally repressed in our cell type, suggesting that LmnB1 OE
promotes gene de-repression. This demonstrates a broader consequence of LmnB1
OE on cell fate, and highlights the importance of maintaining proper levels of
LmnB1.
acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript;
Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing
Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195,
the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run
libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute,
with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg
Initiative Imaging Scientist Award, for electron microscopy sample preparation and
imaging.'
article_number: '2202548'
article_processing_charge: No
article_type: original
author:
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin
organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548
apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression
alters chromatin organization and gene expression. Nucleus. Taylor &
Francis. https://doi.org/10.1080/19491034.2023.2202548
chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1
Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus.
Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.
ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression
alters chromatin organization and gene expression,” Nucleus, vol. 14, no.
1. Taylor & Francis, 2023.
ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters
chromatin organization and gene expression. Nucleus. 14(1), 2202548.
mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization
and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis,
2023, doi:10.1080/19491034.2023.2202548.
short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2023-08-01T14:18:46Z
day: '18'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1080/19491034.2023.2202548
external_id:
isi:
- '000971629400001'
pmid:
- '37071033'
file:
- access_level: open_access
checksum: 8e707eda84f64dbad7f03545ae0a83ef
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:24:55Z
date_updated: 2023-05-02T07:24:55Z
file_id: '12884'
file_name: 2023_Nucleus_Kaneshiro.pdf
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language:
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month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleus
publication_identifier:
eissn:
- 1949-1042
issn:
- 1949-1034
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamin B1 overexpression alters chromatin organization and gene expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12885'
abstract:
- lang: eng
text: 'High-performance semiconductors rely upon precise control of heat and charge
transport. This can be achieved by precisely engineering defects in polycrystalline
solids. There are multiple approaches to preparing such polycrystalline semiconductors,
and the transformation of solution-processed colloidal nanoparticles is appealing
because colloidal nanoparticles combine low cost with structural and compositional
tunability along with rich surface chemistry. However, the multiple processes
from nanoparticle synthesis to the final bulk nanocomposites are very complex.
They involve nanoparticle purification, post-synthetic modifications, and finally
consolidation (thermal treatments and densification). All these properties dictate
the final material’s composition and microstructure, ultimately affecting its
functional properties. This thesis explores the synthesis, surface chemistry and
consolidation of colloidal semiconductor nanoparticles into dense solids. In particular,
the transformations that take place during these processes, and their effect on
the material’s transport properties are evaluated. '
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
citation:
ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation.
2023. doi:10.15479/at:ista:12885'
apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885'
chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.'
ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to
consolidation,” Institute of Science and Technology Austria, 2023.'
ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis
to consolidation. Institute of Science and Technology Austria.'
mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis
to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.'
short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to
Consolidation, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-02T07:58:57Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-08-14T07:25:26Z
day: '28'
ddc:
- '546'
- '541'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaIb
doi: 10.15479/at:ista:12885
ec_funded: 1
file:
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checksum: 9347b0e09425f56fdcede5d3528404dc
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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success: 1
file_date_updated: 2023-05-02T07:43:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '82'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-028-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10806'
relation: part_of_dissertation
status: public
- id: '10042'
relation: part_of_dissertation
status: public
- id: '12237'
relation: part_of_dissertation
status: public
- id: '9118'
relation: part_of_dissertation
status: public
- id: '10123'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12890'
abstract:
- lang: eng
text: We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately geometrically round cultures get a competitive advantage. We first
analyze the model with periodic boundary conditions, where we study how the model
can end up in a fixed state, i.e., freezes. Then we implement the model on the
European geography with mountains and rivers. We see how the model reproduces
some qualitative features of European culture formation, namely, that rivers and
mountains are more frequently borders between cultures, mountainous regions tend
to have higher cultural diversity, and the central European plain has less clear
cultural borders.
acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen
and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support
from the Villum Foundation for support through the QMATH center of Excellence (Grant
No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.
article_number: '054307'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation.
Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307
apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton
model of culture formation. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.108.054307
chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.
ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of
culture formation,” Physical Review E, vol. 108, no. 5. American Physical
Society, 2023.
ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture
formation. Physical Review E. 108(5), 054307.
mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E, vol. 108, no.
5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.
short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).
date_created: 2023-05-04T08:35:01Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-13T07:47:30Z
day: '08'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1103/PhysRevE.108.054307
external_id:
arxiv:
- '2305.02153'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.02153
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/FrederikRavnKlausen/model-for-culture-formation
record:
- id: '12869'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Stochastic cellular automaton model of culture formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-21T06:25:48Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
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date_created: 2023-05-05T13:01:14Z
date_updated: 2023-05-05T13:01:14Z
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file_size: 31434230
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2023-05-05T13:04:15Z
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2023-05-05T13:04:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8966'
relation: part_of_dissertation
status: public
- id: '7888'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12897'
abstract:
- lang: eng
text: "Inverse design problems in fabrication-aware shape optimization are typically
solved on discrete representations such as polygonal meshes. This thesis argues
that there are benefits to treating these problems in the same domain as human
designers, namely, the parametric one. One reason is that discretizing a parametric
model usually removes the capability of making further manual changes to the design,
because the human intent is captured by the shape parameters. Beyond this, knowledge
about a design problem can sometimes reveal a structure that is present in a smooth
representation, but is fundamentally altered by discretizing. In this case, working
in the parametric domain may even simplify the optimization task. We present two
lines of research that explore both of these aspects of fabrication-aware shape
optimization on parametric representations.\r\n\r\nThe first project studies the
design of plane elastic curves and Kirchhoff rods, which are common mathematical
models for describing the deformation of thin elastic rods such as beams, ribbons,
cables, and hair. Our main contribution is a characterization of all curved shapes
that can be attained by bending and twisting elastic rods having a stiffness that
is allowed to vary across the length. Elements like these can be manufactured
using digital fabrication devices such as 3d printers and digital cutters, and
have applications in free-form architecture and soft robotics.\r\n\r\nWe show
that the family of curved shapes that can be produced this way admits geometric
description that is concise and computationally convenient. In the case of plane
curves, the geometric description is intuitive enough to allow a designer to determine
whether a curved shape is physically achievable by visual inspection alone. We
also present shape optimization algorithms that convert a user-defined curve in
the plane or in three dimensions into the geometry of an elastic rod that will
naturally deform to follow this curve when its endpoints are attached to a support
structure. Implemented in an interactive software design tool, the rod geometry
is generated in real time as the user edits a curve and enables fast prototyping.
\r\n\r\nThe second project tackles the problem of general-purpose shape optimization
on CAD models using a novel variant of the extended finite element method (XFEM).
Our goal is the decoupling between the simulation mesh and the CAD model, so no
geometry-dependent meshing or remeshing needs to be performed when the CAD parameters
change during optimization. This is achieved by discretizing the embedding space
of the CAD model, and using a new high-accuracy numerical integration method to
enable XFEM on free-form elements bounded by the parametric surface patches of
the model. Our simulation is differentiable from the CAD parameters to the simulation
output, which enables us to use off-the-shelf gradient-based optimization procedures.
The result is a method that fits seamlessly into the CAD workflow because it works
on the same representation as the designer, enabling the alternation of manual
editing and fabrication-aware optimization at will."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
citation:
ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897'
apa: 'Hafner, C. (2023). Inverse shape design with parametric representations:
Kirchhoff Rods and parametric surface models. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12897'
chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12897.'
ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models,” Institute of Science and Technology Austria,
2023.'
ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. Institute of Science and Technology Austria.'
mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12897.'
short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff
Rods and Parametric Surface Models, Institute of Science and Technology Austria,
2023.'
date_created: 2023-05-05T10:40:14Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-01-29T10:47:51Z
day: '05'
ddc:
- '516'
- '004'
- '518'
- '531'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeBi
doi: 10.15479/at:ista:12897
ec_funded: 1
file:
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checksum: cc2094e92fa27000b70eb4bfb76d6b5a
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:20Z
date_updated: 2023-12-08T23:30:04Z
embargo: 2023-12-07
file_id: '12942'
file_name: thesis-hafner-2023may11-a2b.pdf
file_size: 50714445
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checksum: a6b51334be2b81672357b1549afab40c
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:44Z
date_updated: 2023-12-08T23:30:04Z
embargo_to: open_access
file_id: '12943'
file_name: thesis-release-form.pdf
file_size: 265319
relation: source_file
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has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
isbn:
- 978-3-99078-031-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9817'
relation: part_of_dissertation
status: public
- id: '7117'
relation: part_of_dissertation
status: public
- id: '13188'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric
surface models'
type: dissertation
user_id: 400429CC-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12900'
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:12900
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12900
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.
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:12900.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
date_created: 2023-05-05T11:08:50Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-10-29T09:11:05Z
day: '05'
ddc:
- '537'
- '535'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:12900
ec_funded: 1
file:
- access_level: closed
checksum: 8cbdab9c37ee55e591092a6f66b272c4
content_type: application/x-zip-compressed
creator: rsahu
date_created: 2023-05-09T08:45:14Z
date_updated: 2023-06-06T22:30:03Z
embargo_to: open_access
file_id: '12928'
file_name: thesis.zip
file_size: 36767177
relation: source_file
- access_level: closed
checksum: 439659ead46618147309be39d9dd5a8c
content_type: application/pdf
creator: rsahu
date_created: 2023-05-09T08:51:17Z
date_updated: 2023-07-06T11:37:40Z
file_id: '12929'
file_name: thesis_pdfa_final.pdf
file_size: 17501990
relation: main_file
file_date_updated: 2023-07-06T11:37:40Z
has_accepted_license: '1'
keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
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: '9114'
relation: part_of_dissertation
status: public
- id: '10924'
relation: part_of_dissertation
status: public
- id: '13175'
relation: new_edition
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'
...