---
OA_place: publisher
OA_type: hybrid
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064.
doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp.
1051–1064, 2024.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. 42, 1051–1064.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024,
pp. 1051–64, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.
corr_author: '1'
date_created: 2023-09-03T22:01:15Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T11:27:12Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
isi:
- '001065254200001'
pmid:
- '37653226'
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file_id: '18784'
file_name: 2024_NatureBiotech_Michalska.pdf
file_size: 26065165
relation: main_file
success: 1
file_date_updated: 2025-01-09T07:48:01Z
fulldoi: https://doi.org/10.1038/s41587-023-01911-8
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1051-1064
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
grant_number: LS18-022
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/CATS
record:
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status: deleted
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Imaging brain tissue architecture across millimeter to nanometer scales
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2024'
...
---
OA_place: repository
_id: '18689'
abstract:
- lang: eng
text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
However, simultaneous imaging of multiple fluorophores can result in spectral
leaks and overlapping, which greatly degrades image quality and subsequent analysis.
Existing popular spectral unmixing methods are mainly based on computational intensive
linear models and the performance is heavily dependent on the reference spectra,
which may greatly preclude its further applications. In this paper, we propose
a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
the physical spectral mixing process. A tranfer learning framework is further
devised to allow our AutoUnmix adapting to a variety of imaging systems without
retraining the network. Our proposed method has demonstrated real-time unmixing
capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
speed. We further validate the reconstruction performance on both synthetic datasets
and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
other popular unmixing methods. Due to the desirable property of data independency
and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
and the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 742985, J.F.). It has also
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. bioRxiv. doi:10.1101/2024.02.21.581330
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
in plant roots. bioRxiv. https://doi.org/10.1101/2024.02.21.581330
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” bioRxiv. .
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
10.1101/2024.02.21.581330.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” BioRxiv, doi:10.1101/2024.02.21.581330.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.02.21.581330
language:
- iso: eng
main_file_link:
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month: '02'
oa: 1
oa_version: Preprint
project:
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call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
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call_identifier: H2020
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name: International IST Doctoral Program
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call_identifier: H2020
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name: ISTplus - Postdoctoral Fellowships
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call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
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grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
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relation: dissertation_contains
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researchdata_availability: no
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supplementarymaterial: no
title: Super-resolution expansion microscopy in plant roots
tmp:
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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)
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type: preprint
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year: '2024'
...
---
OA_place: publisher
_id: '18674'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue requires volumetric imaging at nanoscale spatial resolution. While
light microscopy excels at visualizing specific molecules and individual cells,
achieving dense, synapse-level circuit reconstruction has not been possible with
any light microscopy technique. Thus, the goal of my work was to develop image
and data analysis pipelines for brain tissue visualization and reconstruction
with light microscopy. To achieve dense circuit reconstruction with single-synapse
resolution, I developed both conventional and deep-learning-based synapse detection
algorithms, as well as connectivity analysis pipelines that integrate synapse
detection with volumetric segmentation of brain tissue.
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
citation:
ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. 2024. doi:10.15479/at:ista:18674
apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with
super-resolution light microscopy. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18674
chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674.
ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution
light microscopy,” Institute of Science and Technology Austria, 2024.
ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. Institute of Science and Technology Austria.
mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674.
short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-18T14:24:43Z
date_published: 2024-12-18T00:00:00Z
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day: '18'
ddc:
- '004'
degree_awarded: PhD
department:
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- _id: JoDa
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
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issn:
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relation: part_of_dissertation
status: public
- id: '14257'
relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
supplementarymaterial: no
title: Image analysis for brain tissue reconstruction with super-resolution light
microscopy
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_embargo: '20'
OA_place: publisher
_id: '18681'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
citation:
ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy. 2024. doi:10.15479/at:ista:18681'
apa: 'Tavakoli, M. (2024). Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:18681'
chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18681.'
ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain
architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy,” Institute of Science and Technology
Austria, 2024.'
ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and Technology
Austria.'
mla: 'Tavakoli, Mojtaba. Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy. Institute of Science and
Technology Austria, 2024, doi:10.15479/at:ista:18681.'
short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain
Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology
Austria, 2024.'
corr_author: '1'
das_tickbox: '1'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '20'
ddc:
- '600'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18681
doi_confirm: '1'
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language:
- iso: eng
month: '12'
oa_version: Published Version
page: '230'
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-048-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11160'
relation: part_of_dissertation
status: public
- id: '18688'
relation: part_of_dissertation
status: public
- id: '18689'
relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
researchdata_availability: unclear
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
supplementarymaterial: unclear
title: 'Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
_id: '18677'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labeling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: E-Lib
- _id: M-Shop
- _id: LifeSc
- _id: Bio
- _id: ScienComp
acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript.
We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics,
Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and
Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian
Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC
fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions
Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n"
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense
connectomic reconstruction of mammalian brain tissue. bioRxiv. doi:10.1101/2024.03.01.582884
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic
reconstruction of mammalian brain tissue. bioRxiv. https://doi.org/10.1101/2024.03.01.582884
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy
Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv,
n.d. https://doi.org/10.1101/2024.03.01.582884.
ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction
of mammalian brain tissue,” bioRxiv. .
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue. bioRxiv, 10.1101/2024.03.01.582884.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.03.01.582884
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.03.01.582884
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19704'
relation: later_version
status: public
- id: '18674'
relation: dissertation_contains
status: public
- id: '18681'
relation: dissertation_contains
status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
_id: '18688'
abstract:
- lang: eng
text: The human brain has remarkable computational power. It generates sophisticated
behavioral sequences, stores engrams over an individual’s lifetime, and produces
higher cognitive functions up to the level of consciousness. However, so little
of our neuroscience knowledge covers the human brain, and it remains unknown whether
this organ is truly unique, or is a scaled version of the extensively studied
rodent brain. To address this fundamental question, we determined the cellular,
synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using
multicellular patch clamp-recording. This circuit is the largest autoassociative
network in the brain, and plays a key role in memory and higher-order computations
such as pattern separation and pattern completion. We demonstrate that human hippocampal
CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks.
Connectivity sparsifies from rodents to humans, providing a circuit architecture
that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses
showed both distinct species-specific and circuit-dependent properties, with high
reliability, unique amplitude precision, and long integration times. We also identify
differential scaling rules between hippocampal pathways from rodents to humans,
with a moderate increase in the convergence of CA3 inputs per cell, but a marked
increase in human mossy fiber innervation. Anatomically guided full-scale modeling
suggests that the human brain’s sparse connectivity, expanded neuronal number,
and reliable synaptic signaling combine to enhance the associative memory storage
capacity of CA3. Together, our results reveal unique rules of connectivity and
synaptic signaling in the human hippocampus, demonstrating the absolute necessity
of human brain research and beginning to unravel the remarkable performance of
our autoassociative memory circuits.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: PreCl
- _id: ScienComp
acknowledgement: We thank Florian Marr for excellent technical assistance, Christina
Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor
Asenov for development of the transportation box for human brain tissue, Tim Vogels
for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from
Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life
Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge
the excellent support of the Medical University of Vienna Department of Neurosurgery
staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry,
and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie
Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund
(FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian
Academy of Sciences (DOC fellowship 26137 to M.R.T.).
article_processing_charge: No
author:
- first_name: Jake F.
full_name: Watson, Jake F.
last_name: Watson
- first_name: Victor
full_name: Vargas-Barroso, Victor
last_name: Vargas-Barroso
- first_name: Rebecca J.
full_name: Morse-Mora, Rebecca J.
last_name: Morse-Mora
- first_name: Andrea
full_name: Navas-Olive, Andrea
last_name: Navas-Olive
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Matthias
full_name: Tomschik, Matthias
last_name: Tomschik
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses
specific functional connectivity rules for efficient associative memory. bioRxiv.
doi:10.1101/2024.05.02.592169
apa: Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli,
M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv. https://doi.org/10.1101/2024.05.02.592169
chicago: Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive,
Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M
Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for
Efficient Associative Memory.” BioRxiv, n.d. https://doi.org/10.1101/2024.05.02.592169.
ieee: J. F. Watson et al., “Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory,” bioRxiv. .
ista: Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl
JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv, 10.1101/2024.05.02.592169.
mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
Rules for Efficient Associative Memory.” BioRxiv, doi:10.1101/2024.05.02.592169.
short: J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli,
J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T11:35:08Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-10-02T11:27:43Z
day: '02'
department:
- _id: JoDa
- _id: PeJo
doi: 10.1101/2024.05.02.592169
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.05.02.592169
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.05.02.592169
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '18879'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Human hippocampal CA3 uses specific functional connectivity rules for efficient
associative memory
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '17133'
abstract:
- lang: eng
text: "An ideal quantum computer relies on qubits capable of performing fast gate
operations and\r\nmaintaining strong interconnections while preserving their quantum
coherence. Since the\r\ninception of experimental eforts toward building a quantum
computer, the community has\r\nfaced challenges in engineering such a system.
Among the various methods of implementing a\r\nquantum computer, superconducting
qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art
reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously
long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith
high coherence require isolation from the environment, while fast operation necessitates\r\nstrong
coupling of the qubit. This thesis approaches this issue by proposing the idea
of\r\nengineering superconducting qubits capable of transitioning between operating
in a protected\r\nregime, where the qubit is completely isolated from the environment,
and coupling to the\r\ncommunication channels as needed. In this direction, we
use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices,
searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis
leads us to the inductively shunted transmon (IST) regime, characterized by EJ
/EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well
with a large barrier\r\nseparating the local ground states of each quantum well.
In this regime, although it is\r\nanticipated that the two quantum wells would
be isolated from each other, we observe single\r\nfuxon tunneling between them.
The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical
system, containing resonance conditions that allow the preparation of the\r\nfuxon
ground or excited states. This enables us to study the relaxation rate of such
transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling
the barrier height\r\nbetween the two quantum wells allows for controllable coupling,
which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe
0-π qubit is one of the very few known superconducting circuit types that ofers
exponential\r\nprotection from both relaxation and dephasing simultaneously. However,
this qubit is not\r\nexempt from the fact that such protection comes at the expense
of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably
break the circuit symmetry, the\r\nkey reason for the protection, to momentarily
restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances
and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling
of the protected state to the thermally occupied parasitic mode\r\nof the circuit.
However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand
show that this can be used as a tunable coupler between the protected states.
In the\r\nfuture, this should allow to perform gate operations by dynamically
controlling the asymmetry\r\ninstead of driving the protected transition with
microwave pulses. Therefore, we believe that\r\nthe proposed method can make the
use of protected qubits more practical in experimental\r\nrealizations of quantum
computing."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
citation:
ama: Hassani F. Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes. 2024. doi:10.15479/at:ista:17133
apa: Hassani, F. (2024). Superconducting qubits capable of dynamic switching
between protected and high-speed control regimes. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:17133
chicago: Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:17133.
ieee: F. Hassani, “Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes,” Institute of Science and Technology Austria,
2024.
ista: Hassani F. 2024. Superconducting qubits capable of dynamic switching between
protected and high-speed control regimes. Institute of Science and Technology
Austria.
mla: Hassani, Farid. Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:17133.
short: F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected
and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-06-11T18:20:05Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2026-10-02T11:28:17Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:17133
doi_confirm: '1'
file:
- access_level: open_access
checksum: 258c353d47fa37ea63ea43b1e10a34a0
content_type: application/pdf
creator: fhassani
date_created: 2024-06-12T07:53:19Z
date_updated: 2024-06-20T11:52:22Z
file_id: '17137'
file_name: Thesis_main_final.pdf
file_size: 28370759
relation: main_file
- access_level: closed
checksum: deffa5d0db88093f74812fa71520d5e1
content_type: text/x-tex
creator: fhassani
date_created: 2024-06-12T07:54:27Z
date_updated: 2024-06-12T07:54:27Z
file_id: '17138'
file_name: Thesis_main.tex
file_size: 445735
relation: source_file
file_date_updated: 2024-06-20T11:52:22Z
fulldoi: https://doi.org/10.15479/at:ista:17133
has_accepted_license: '1'
keyword:
- Quantum information
- Qubits
- Superconducting devices
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '161'
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-040-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13227'
relation: part_of_dissertation
status: public
- id: '9928'
relation: part_of_dissertation
status: public
- id: '8755'
relation: part_of_dissertation
status: public
researchdata_availability: no
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
supplementarymaterial: no
title: Superconducting qubits capable of dynamic switching between protected and high-speed
control regimes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
DOAJ_listed: '1'
_id: '14852'
abstract:
- lang: eng
text: The physical conditions giving rise to high escape fractions of ionizing radiation
(LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization
– are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α
emitters at 2.9 < z < 6.7, we compare stacked rest-frame UV spectra
of candidates for LyC leakers and non-leakers selected based on their Ly α profiles.
We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric
Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666,
[Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization
state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640
(∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533
emission, revealing substantial amounts of neutral hydrogen off the line of sight;
(iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75)
, signalling the presence of low column density channels in the ISM. In contrast,
the stacks with broad, asymmetric Ly α profiles with large peak separation show
weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low
C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen
column densities. Our results suggest that C iv/C iii] might be sensitive to the
physical conditions that govern LyC photon escape, providing a promising tool
for identification of ionizing sources among star-forming galaxies in the epoch
of reionization.
acknowledgement: 'We thank the anonymous referee for the constructive feedback that
helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte
Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions.
We also thank the organizers and participants of the 24th MUSE Science Busy Week
in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty
of Science of the University of Geneva. This work has received funding from the
Swiss State Secretariat for Education, Research and Innovation (SERI) under contract
number MB22.00072, as well as from the Swiss National Science Foundation (SNSF)
through project grant number 200020_207349 and SNSF Professorship grant number 190079.
The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation
under grant number 140. This paper is based on observations collected at the European
Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes
094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240,
096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source
software packages and we are thankful to the respective authors for sharing their
work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB
(Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Kramarenko, Ivan
id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4
last_name: Kramarenko
orcid: 0000-0001-5346-6048
- first_name: J
full_name: Kerutt, J
last_name: Kerutt
- first_name: A
full_name: Verhamme, A
last_name: Verhamme
- first_name: P A
full_name: Oesch, P A
last_name: Oesch
- first_name: L
full_name: Barrufet, L
last_name: Barrufet
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: H
full_name: Kusakabe, H
last_name: Kusakabe
- first_name: I
full_name: Goovaerts, I
last_name: Goovaerts
- first_name: T T
full_name: Thai, T T
last_name: Thai
citation:
ama: Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of
MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices
of the Royal Astronomical Society. 2024;527(4):9853-9871. doi:10.1093/mnras/stad3853
apa: Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee,
J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters
at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical
Society. Oxford University Press. https://doi.org/10.1093/mnras/stad3853
chicago: Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J
Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties
of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices
of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stad3853.
ieee: I. Kramarenko et al., “Linking UV spectral properties of MUSE Ly α
emitters at z ≳ 3 to Lyman continuum escape,” Monthly Notices of the
Royal Astronomical Society, vol. 527, no. 4. Oxford University Press, pp.
9853–9871, 2024.
ista: Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe
H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters
at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical
Society. 527(4), 9853–9871.
mla: Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters
at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical
Society, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:10.1093/mnras/stad3853.
short: I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee,
H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical
Society 527 (2024) 9853–9871.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Raw MUSE data cubes are available from the ESO Science
Archive Facility.2 The MUSE-Wide data from the first data release, which covers
44 fields in GOODS-S/CDFS, are available on the MUSE-Wide project page.3 The MUSE
HUDF data from the second data release are available via the Advanced MUSE Data
products (AMUSED) web interface.4 The stacked spectra in a machine-readable format
and the spectral line measurements will be shared upon request to the corresponding
author.
date_created: 2024-01-22T08:22:17Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2026-10-02T11:29:18Z
day: '01'
ddc:
- '520'
department:
- _id: GradSch
- _id: JoMa
doi: 10.1093/mnras/stad3853
external_id:
arxiv:
- '2305.07044'
isi:
- '001133672400004'
file:
- access_level: open_access
checksum: 9d02df4035c4951cf63dee0db1e462e9
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T12:30:45Z
date_updated: 2024-01-23T12:30:45Z
file_id: '14879'
file_name: 2024_MNAstronomSoc_Kramarenko.pdf
file_size: 4521738
relation: main_file
success: 1
file_date_updated: 2024-01-23T12:30:45Z
fulldoi: https://doi.org/10.1093/mnras/stad3853
has_accepted_license: '1'
intvolume: ' 527'
isi: 1
issue: '4'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 9853-9871
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: no
title: Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman
continuum escape
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 527
year: '2024'
...
---
OA_type: closed access
_id: '18266'
abstract:
- lang: eng
text: Matrix games are the most basic model in game theory, and yet robustness with
respect to small perturbations of the matrix entries is not fully understood.
In this paper, we introduce value positivity and uniform value positivity, two
properties that refine the notion of optimality in the context of polynomially
perturbed matrix games. The first concept captures how the value depends on the
perturbation parameter, and the second consists of the existence of a fixed strategy
that guarantees the value of the unperturbed matrix game for every sufficiently
small positive parameter. We provide polynomial-time algorithms to check whether
a polynomially perturbed matrix game satisfies these properties. We further provide
the functional form for a parameterized optimal strategy and the value function.
Finally, we translate our results to linear programming and stochastic games,
where value positivity is related to the existence of robust solutions.
acknowledgement: This research was supported by Fondation CFM pour la Recherche, the
H2020 European Research Council [Grant ERC-CoG-863818 (ForM-SMArt)], the Austrian
Science Fund [Grant 10.55776/COE12], ANID Chile [Grant ACT210005], and Agence Nationale
de la Recherche [Grant ANR-21-CE40-0020].
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Miquel
full_name: Oliu-Barton, Miquel
last_name: Oliu-Barton
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
citation:
ama: Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. Value-positivity for matrix
games. Mathematics of Operations Research. 2024;50(4):2433-3282. doi:10.1287/moor.2022.0332
apa: Chatterjee, K., Oliu-Barton, M., & Saona Urmeneta, R. J. (2024). Value-positivity
for matrix games. Mathematics of Operations Research. Institute for Operations
Research and the Management Sciences. https://doi.org/10.1287/moor.2022.0332
chicago: Chatterjee, Krishnendu, Miquel Oliu-Barton, and Raimundo J Saona Urmeneta.
“Value-Positivity for Matrix Games.” Mathematics of Operations Research.
Institute for Operations Research and the Management Sciences, 2024. https://doi.org/10.1287/moor.2022.0332.
ieee: K. Chatterjee, M. Oliu-Barton, and R. J. Saona Urmeneta, “Value-positivity
for matrix games,” Mathematics of Operations Research, vol. 50, no. 4.
Institute for Operations Research and the Management Sciences, pp. 2433–3282,
2024.
ista: Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. 2024. Value-positivity for
matrix games. Mathematics of Operations Research. 50(4), 2433–3282.
mla: Chatterjee, Krishnendu, et al. “Value-Positivity for Matrix Games.” Mathematics
of Operations Research, vol. 50, no. 4, Institute for Operations Research
and the Management Sciences, 2024, pp. 2433–3282, doi:10.1287/moor.2022.0332.
short: K. Chatterjee, M. Oliu-Barton, R.J. Saona Urmeneta, Mathematics of Operations
Research 50 (2024) 2433–3282.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-10-09T07:02:20Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-10-02T11:30:08Z
day: '01'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1287/moor.2022.0332
ec_funded: 1
external_id:
isi:
- '001328875900001'
fulldoi: https://doi.org/10.1287/moor.2022.0332
intvolume: ' 50'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 2433-3282
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Mathematics of Operations Research
publication_identifier:
eissn:
- 1526-5471
issn:
- 0364-765X
publication_status: published
publisher: Institute for Operations Research and the Management Sciences
quality_controlled: '1'
related_material:
record:
- id: '20234'
relation: dissertation_contains
status: public
researchdata_availability: unclear
scopus_import: '1'
status: public
supplementarymaterial: unclear
title: Value-positivity for matrix games
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 50
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17047'
abstract:
- lang: eng
text: We provide a dynamical study of a model of multiplicative perturbation of
a unitary matrix introduced by Fyodorov. In particular, we identify a flow of
deterministic domains that bound the spectrum with high probability, separating
the outlier from the typical eigenvalues at all sub-critical timescales. These
results are obtained under generic assumptions on U that hold for a variety of
unitary random matrix models.
article_number: '2450007'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Guillaume
full_name: Dubach, Guillaume
id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E
last_name: Dubach
orcid: 0000-0001-6892-8137
- first_name: Jana
full_name: Reker, Jana
id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9
last_name: Reker
citation:
ama: 'Dubach G, Reker J. Dynamics of a rank-one multiplicative perturbation of a
unitary matrix. Random Matrices: Theory and Applications. 2024;13(2). doi:10.1142/s2010326324500072'
apa: 'Dubach, G., & Reker, J. (2024). Dynamics of a rank-one multiplicative
perturbation of a unitary matrix. Random Matrices: Theory and Applications.
World Scientific Publishing. https://doi.org/10.1142/s2010326324500072'
chicago: 'Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative
Perturbation of a Unitary Matrix.” Random Matrices: Theory and Applications.
World Scientific Publishing, 2024. https://doi.org/10.1142/s2010326324500072.'
ieee: 'G. Dubach and J. Reker, “Dynamics of a rank-one multiplicative perturbation
of a unitary matrix,” Random Matrices: Theory and Applications, vol. 13,
no. 2. World Scientific Publishing, 2024.'
ista: 'Dubach G, Reker J. 2024. Dynamics of a rank-one multiplicative perturbation
of a unitary matrix. Random Matrices: Theory and Applications. 13(2), 2450007.'
mla: 'Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative
Perturbation of a Unitary Matrix.” Random Matrices: Theory and Applications,
vol. 13, no. 2, 2450007, World Scientific Publishing, 2024, doi:10.1142/s2010326324500072.'
short: 'G. Dubach, J. Reker, Random Matrices: Theory and Applications 13 (2024).'
corr_author: '1'
das_tickbox: '0'
date_created: 2024-05-23T08:31:57Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-02T11:31:29Z
day: '01'
department:
- _id: GradSch
- _id: LaEr
doi: 10.1142/s2010326324500072
ec_funded: 1
external_id:
arxiv:
- '2212.14638'
isi:
- '001229295200002'
fulldoi: https://doi.org/10.1142/s2010326324500072
intvolume: ' 13'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2212.14638'
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: 'Random Matrices: Theory and Applications'
publication_identifier:
eissn:
- 2010-3271
issn:
- 2010-3263
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
related_material:
record:
- id: '17164'
relation: dissertation_contains
status: public
researchdata_availability: unclear
scopus_import: '1'
status: public
supplementarymaterial: unclear
title: Dynamics of a rank-one multiplicative perturbation of a unitary matrix
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18891'
abstract:
- lang: eng
text: "Deep neural networks (DNNs) exhibit a surprising structure in their final
layer\r\nknown as neural collapse (NC), and a growing body of works has currently
investigated the propagation of neural collapse to earlier layers of DNNs – a
phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical
results are restricted to special cases: linear models, only two layers or binary
classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth
in multi-class classification and reveal a surprising qualitative shift. As soon
as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the
deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework
for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer
regularization schemes: this bias\r\nleads to optimal solutions of even lower
rank than the neural collapse. We support\r\nour theoretical findings with experiments
on both DUFM and real data, which show\r\nthe emergence of the low-rank structure
in the solution found by gradient descent."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize.
This research was supported by the Scientific Service Units (SSU) of ISTA through
resources provided by Scientific Computing (SciComp).
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Peter
full_name: Súkeník, Peter
id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c
last_name: Súkeník
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is
deep neural collapse really optimal? In: 38th Annual Conference on Neural Information
Processing Systems. Vol 37. Neural Information Processing Systems Foundation;
2024.'
apa: 'Súkeník, P., Lampert, C., & Mondelli, M. (2024). Neural collapse versus
low-rank bias: Is deep neural collapse really optimal? In 38th Annual Conference
on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural
Information Processing Systems Foundation.'
chicago: 'Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse
versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In 38th Annual
Conference on Neural Information Processing Systems, Vol. 37. Neural Information
Processing Systems Foundation, 2024.'
ieee: 'P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank
bias: Is deep neural collapse really optimal?,” in 38th Annual Conference on
Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37.'
ista: 'Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias:
Is deep neural collapse really optimal? 38th Annual Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in
Neural Information Processing Systems, vol. 37.'
mla: 'Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural
Collapse Really Optimal?” 38th Annual Conference on Neural Information Processing
Systems, vol. 37, Neural Information Processing Systems Foundation, 2024.'
short: P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural
Information Processing Systems, Neural Information Processing Systems Foundation,
2024.
conference:
end_date: 2024-12-16
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2024-12-16
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-27T11:15:18Z
date_published: 2024-12-01T00:00:00Z
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- _id: MaMo
- _id: ChLa
external_id:
arxiv:
- '2405.14468'
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project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 38th Annual Conference on Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
researchdata_availability: no
status: public
supplementarymaterial: no
title: 'Neural collapse versus low-rank bias: Is deep neural collapse really optimal?'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2024'
...
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abstract:
- lang: eng
text: "Understanding the role of evolutionary processes in shaping genetic variation
has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question
is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby
generating genetic and\r\nphenotypic divergence and reproductive isolation (RI).
This requires quantifying the role\r\nand relative contributions of prezygotic
and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between
populations, and identifying regions in the genome\r\nthat mediate RI, which is
often polygenic. Further, this needs distinguishing neutral and\r\nselected regions
in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation
structure, defined as any deviation from panmixia, such as geographic distribution,
movement and mating patterns of individuals, influences how genetic variation
is\r\nstructured in space and shapes the neutral null model. Availability of large
scale spatial\r\ngenomic datasets now enables us to detect signatures of population
structure in genetic\r\ndata and infer population genetic parameters. Such inferences
are crucial and have wide\r\napplications in biodiversity, conservation genetics,
population management and medical\r\ngenetics. However, inferences are based on
assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous
conclusions. Moreover, the role and interaction\r\nof heterogeneous population
density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging
to study owing to their mathematical complexity. In such scenarios,\r\nfeedback
between theory, data and simulations can prove to be useful.\r\nIn this thesis,
I examine the effect of population structure on neutral genetic variation\r\nand
barriers to gene exchange in hybridising populations, thereby bridging together
the\r\nfields of spatial population genetics and speciation.\r\nDespite being
a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition
and has been used and measured differently across different fields. Chapter 2\r\ngives
a quantitative definition of RI, in terms of the effect of genetic differences
on gene\r\nflow. We give analytical predictions for RI in a range of scenarios,
in terms of effective migration rates for discrete populations and barrier strength
for continuous populations.\r\nIn addition to this, we discuss current measures
of RI and their limitations, and propose\r\nthe need for new measures that combine
organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined
effect of assortative mating, sexual selection\r\nand viability selection on RI.
For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model.
We obtain novel theoretical predictions for molecular divergence\r\nin terms of
effective migration rates, which bears a simple relationship to measurable\r\nfitness
components of migrants and various early generation hybrids. We explore the\r\nconditions
under which local adaptation can be maintained despite maladaptive gene flow\r\nand
quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers
to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of
Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m.
pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested
that flower colour is target of\r\npollinator mediated selection and is influenced
only by few genes. While these regions\r\nshow high genetic differentiation between
the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4
examines the effects of heterogeneous population density\r\nand leptokurtic dispersal
on isolation by distance and the distribution of heterozygosity\r\nby focusing
on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations
among 6 focal flower colour markers to\r\nunderstand how selection and dispersal
maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci
and positive associations throughout the hybrid zone, contrary to\r\nthe expected
patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined
with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers
to gene flow, but are rather a result of long-distance migration. This framework\r\nallows
us to get realistic estimates gene flow and selection and shows how traditional
cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory
are not met.\r\nOverall, this thesis investigates how different features of population
structure leave\r\ndetectable signatures in genetic variation, namely in patterns
of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It
also highlights how effective migration\r\nrates provide useful way of analysing
polygenic architectures and shed new light into\r\nhybrid zones. In doing so,
I identify scenarios when simple models become insufficient\r\nand suggest possibe
directions by combining genetic data with simulations."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral
Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02)
for financially\r\nsupporting my research over the years."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
citation:
ama: Surendranadh P. Effect of population structure on neutral genetic variation
and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515
apa: Surendranadh, P. (2024). Effect of population structure on neutral genetic
variation and barriers to gene exchange. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:18515
chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18515.
ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation
and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.
ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation
and barriers to gene exchange. Institute of Science and Technology Austria.
mla: Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:18515.
short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation
and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '1'
date_created: 2024-11-06T21:25:37Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2026-10-02T11:36:48Z
day: '07'
ddc:
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doi_confirm: '1'
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month: '11'
oa: 1
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grant_number: P32166
name: Snapdragon Speciation
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grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
researchdata_availability: yes
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
supplementarymaterial: no
title: Effect of population structure on neutral genetic variation and barriers to
gene exchange
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short: CC BY-NC-SA (4.0)
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...
---
APC_amount: 3028,31 EUR
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OA_place: publisher
OA_type: gold
_id: '18087'
abstract:
- lang: eng
text: We present a theory describing the interaction of structured light, such as
light carrying orbital angular momentum, with molecules. The light-matter interaction
Hamiltonian we derive is expressed through couplings between spherical gradients
of the electric field and the (transition) electric multipole moments of a particle
of any nontrivial rotation point group. Our model can therefore accommodate an
arbitrary complexity of the molecular and electric field structure, and it can
be straightforwardly extended to atoms or nanostructures. Applying this framework
to rovibrational spectroscopy of molecules, we uncover the general mechanism of
angular momentum exchange between the spin and orbital angular momenta of light,
molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity
of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions
that are considered forbidden in the case of nonhelical light. We discuss the
experimental requirements for the observation of these forbidden transitions in
state-of-the-art spatially resolved spectroscopy measurements.
acknowledgement: We are grateful to Emilio Pisanty and Philipp Lunt for valuable discussions.
This research was funded wholly or in part by the Austrian Science Fund (FWF) [10.55776/F1004].
G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.
M.L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON). O.H.H. acknowledges support by the Austrian Science Fund (FWF)
[10.55776/P36040]. Furthermore, the financial support by the Austrian Federal Ministry
for Digital and Economic Affairs, the National Foundation for Research, Technology
and Development, and the Christian Doppler Research Association is gratefully acknowledged.
article_number: '033277'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: Mateja
full_name: Hrast, Mateja
id: 48dbb294-2a9c-11ef-905d-f56be71f0e5d
last_name: Hrast
- first_name: Oliver H.
full_name: Heckl, Oliver H.
last_name: Heckl
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. Theory of angular momentum
transfer from light to molecules. Physical Review Research. 2024;6(3).
doi:10.1103/physrevresearch.6.033277
apa: Maslov, M., Koutentakis, G., Hrast, M., Heckl, O. H., & Lemeshko, M. (2024).
Theory of angular momentum transfer from light to molecules. Physical Review
Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.033277
chicago: Maslov, Mikhail, Georgios Koutentakis, Mateja Hrast, Oliver H. Heckl, and
Mikhail Lemeshko. “Theory of Angular Momentum Transfer from Light to Molecules.”
Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.033277.
ieee: M. Maslov, G. Koutentakis, M. Hrast, O. H. Heckl, and M. Lemeshko, “Theory
of angular momentum transfer from light to molecules,” Physical Review Research,
vol. 6, no. 3. American Physical Society, 2024.
ista: Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. 2024. Theory of angular
momentum transfer from light to molecules. Physical Review Research. 6(3), 033277.
mla: Maslov, Mikhail, et al. “Theory of Angular Momentum Transfer from Light to
Molecules.” Physical Review Research, vol. 6, no. 3, 033277, American Physical
Society, 2024, doi:10.1103/physrevresearch.6.033277.
short: M. Maslov, G. Koutentakis, M. Hrast, O.H. Heckl, M. Lemeshko, Physical Review
Research 6 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-18T11:43:16Z
date_published: 2024-09-10T00:00:00Z
date_updated: 2026-10-02T11:36:24Z
day: '10'
ddc:
- '530'
department:
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevresearch.6.033277
ec_funded: 1
external_id:
arxiv:
- '2310.00095'
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issue: '3'
language:
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month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3
grant_number: F100403
name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
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call_identifier: FWF
name: FWF Open Access Fund
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publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
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supplementarymaterial: yes
title: Theory of angular momentum transfer from light to molecules
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user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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...
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_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2026-10-02T11:40:30Z
day: '23'
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- '519'
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department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
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keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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researchdata_availability: no
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supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
supplementarymaterial: no
title: Genetic information and biological optimization
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
_id: '17225'
abstract:
- lang: eng
text: "This thesis describes the development of an atom interferometer designed
to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision
measurements beyond\r\nthe standard quantum limit. While the project remains ongoing,
significant progress has been\r\nmade.\r\nA key contribution of this work is the
development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ
framework. This software enables precise timing and control\r\nwithout requiring
prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe
interface offers user friendly visual comprehension of the experimental sequence
and\r\nextended capabilities, allowing researchers to scan variables with a simple
click of a mouse.\r\nThe main proposed project is to implement atom interferometric
sequence with squeezed input\r\nstates inside of a dipole trap generated by a
high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional
atomic cloud split while maintaining relatively strong confinement\r\nin other
directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro
kelvin temperatures, load\r\nthem into the dipole trap and state prepare them
to be used for squeezing and interferometric\r\nsequence."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vyacheslav
full_name: Li, Vyacheslav
id: 3A4FAA92-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:10.15479/at:ista:17225
apa: Li, V. (2024). Towards a quantum entanglement enhanced atom interferomter.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17225
chicago: Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17225.
ieee: V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute
of Science and Technology Austria, 2024.
ista: Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute
of Science and Technology Austria.
mla: Li, Vyacheslav. Towards a Quantum Entanglement Enhanced Atom Interferomter.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17225.
short: V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute
of Science and Technology Austria, 2024.
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text: "This thesis consists of two separate parts. In the first part we consider
a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$.
Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the
setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion
principle plays a key role. We show that, at zero temperature, the ground state
energy density of the interacting spin-polarized gas differs (to leading order)
from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$
\ with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$
the density. Further, we extend this to positive temperature and show that the
pressure of an interacting spin-polarized gas differs from that of the free gas
by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly,
we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions
and show that here, as an upper bound, the ground state energy density differs
from that of the free system by a term of order $a_s \\rho^2$ with an error smaller
than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$
is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese
asymptotic formulas complement the similar formulas in the literature for the
dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies
or pressures differ from that of the corresponding free systems by a term of order
$a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections,
of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires
a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider
the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular
its associated critical temperature and energy gap. We prove that the ratio of
the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches
a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high
density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$.
This complements the proofs in the literature of this universal behaviour in the
limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that
the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$
approaches a universal function of the relative temperature $T/T_c$ in the limit
of weak coupling in dimensions $d=1,2,3$."
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citation:
ama: Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory.
2024. doi:10.15479/at:ista:18135
apa: Lauritsen, A. B. (2024). Energies of dilute Fermi gases and universalities
in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18135
chicago: Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities
in BCS Theory.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18135.
ieee: A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS
theory,” Institute of Science and Technology Austria, 2024.
ista: Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS
theory. Institute of Science and Technology Austria.
mla: Lauritsen, Asbjørn Bækgaard. Energies of Dilute Fermi Gases and Universalities
in BCS Theory. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18135.
short: A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS
Theory, Institute of Science and Technology Austria, 2024.
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supervisor:
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title: Energies of dilute Fermi gases and universalities in BCS theory
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abstract:
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text: "It is a remarkable property of BCS theory that the ratio of the energy gap
at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given
by a universal constant, independent of the microscopic details of the fermionic
interaction. This universality has rigorously been proven quite recently in three
spatial dimensions and three different limiting regimes: weak coupling, low density
and high density. The goal of this short note is to extend the universal behavior
to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."
acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully
acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No.
101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber
I6427.
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author:
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full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
citation:
ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory.
Reviews in Mathematical Physics. 2024;36(9). doi:10.1142/s0129055x2360005x
apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2024). Universality in low-dimensional
BCS theory. Reviews in Mathematical Physics. World Scientific Publishing.
https://doi.org/10.1142/s0129055x2360005x
chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality
in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World
Scientific Publishing, 2024. https://doi.org/10.1142/s0129055x2360005x.
ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional
BCS theory,” Reviews in Mathematical Physics, vol. 36, no. 9. World Scientific
Publishing, 2024.
ista: Henheik SJ, Lauritsen AB, Roos B. 2024. Universality in low-dimensional BCS
theory. Reviews in Mathematical Physics. 36(9), 2360005.
mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.”
Reviews in Mathematical Physics, vol. 36, no. 9, 2360005, World Scientific
Publishing, 2024, doi:10.1142/s0129055x2360005x.
short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics 36
(2024).
corr_author: '1'
das_tickbox: '0'
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ddc:
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- _id: LaEr
- _id: RoSe
doi: 10.1142/s0129055x2360005x
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grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
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publisher: World Scientific Publishing
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supplementarymaterial: no
title: Universality in low-dimensional BCS theory
tmp:
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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)
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...
---
_id: '14931'
abstract:
- lang: eng
text: We prove an upper bound on the ground state energy of the dilute spin-polarized
Fermi gas capturing the leading correction to the kinetic energy resulting from
repulsive interactions. One of the main ingredients in the proof is a rigorous
implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].
acknowledgement: A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej
for valuable discussions. We thank Alessandro Giuliani for helpful discussions and
for pointing out the reference [18]. Funding from the European Union's Horizon 2020
research and innovation programme under the ERC grant agreement No 694227 is acknowledged.
Financial support by the Austrian Science Fund (FWF) through project number I 6427-N
(as part of the SFB/TRR 352) is gratefully acknowledged.
article_number: '110320'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
2024;286(7). doi:10.1016/j.jfa.2024.110320'
apa: 'Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute
spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320'
chicago: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy
of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.'
ieee: 'A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis,
vol. 286, no. 7. Elsevier, 2024.'
ista: 'Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
286(7), 110320.'
mla: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of
the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.'
short: A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: No data was used for the research described in the article.
date_created: 2024-02-04T23:00:53Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-02T11:43:00Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2024.110320
ec_funded: 1
external_id:
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- '2301.04894'
isi:
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grant_number: '694227'
name: Analysis of quantum many-body systems
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supplementarymaterial: no
title: 'Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via
cluster expansion'
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
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---
_id: '18107'
abstract:
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text: We consider a dilute fully spin-polarized Fermi gas at positive temperature
in dimensions d∈{1,2,3} . We show that the pressure of the interacting gas is
bounded from below by that of the free gas plus, to leading order, an explicit
term of order adρ2+2/d, where a is the p-wave scattering length of the repulsive
interaction and ρ is the particle density. The results are valid for a wide
range of repulsive interactions, including that of a hard core, and uniform in
temperatures at most of the order of the Fermi temperature. A central ingredient
in the proof is a rigorous implementation of the fermionic cluster expansion of
Gaudin, Gillespie and Ripka (Nucl. Phys. A, 176.2 (1971), pp. 237–260).
acknowledgement: 'Financial support by the Austrian Science Fund (FWF) through grant
DOI: 10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged.'
article_number: e78
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Lauritsen AB, Seiringer R. Pressure of a dilute spin-polarized Fermi gas:
Lower bound. Forum of Mathematics, Sigma. 2024;12. doi:10.1017/fms.2024.56'
apa: 'Lauritsen, A. B., & Seiringer, R. (2024). Pressure of a dilute spin-polarized
Fermi gas: Lower bound. Forum of Mathematics, Sigma. Cambridge University
Press. https://doi.org/10.1017/fms.2024.56'
chicago: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute
Spin-Polarized Fermi Gas: Lower Bound.” Forum of Mathematics, Sigma. Cambridge
University Press, 2024. https://doi.org/10.1017/fms.2024.56.'
ieee: 'A. B. Lauritsen and R. Seiringer, “Pressure of a dilute spin-polarized Fermi
gas: Lower bound,” Forum of Mathematics, Sigma, vol. 12. Cambridge University
Press, 2024.'
ista: 'Lauritsen AB, Seiringer R. 2024. Pressure of a dilute spin-polarized Fermi
gas: Lower bound. Forum of Mathematics, Sigma. 12, e78.'
mla: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute Spin-Polarized
Fermi Gas: Lower Bound.” Forum of Mathematics, Sigma, vol. 12, e78, Cambridge
University Press, 2024, doi:10.1017/fms.2024.56.'
short: A.B. Lauritsen, R. Seiringer, Forum of Mathematics, Sigma 12 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-20T12:25:25Z
date_published: 2024-09-09T00:00:00Z
date_updated: 2026-10-02T11:43:00Z
day: '09'
ddc:
- '510'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1017/fms.2024.56
external_id:
arxiv:
- '2407.05990'
isi:
- '001307817400001'
file:
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relation: main_file
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has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
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month: '09'
oa: 1
oa_version: Published Version
project:
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '18135'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Pressure of a dilute spin-polarized Fermi gas: Lower bound'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2024'
...
---
OA_place: publisher
OA_type: free access
_id: '18443'
abstract:
- lang: eng
text: "In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry
relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli
spaces. As a consequence, they\r\nconjecture an equivalence between categories
of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given
by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable
systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler
structures and the\r\ncorresponding branes on affine torus bundles. We use the
techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures
are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for
generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality
between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles
and connections. This T-duality in the appropriate context specializes to\r\nT-duality
between BBB and BAA-branes.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maria A
full_name: Sisak, Maria A
id: 44A03D04-AEA4-11E9-B225-EA2DE6697425
last_name: Sisak
citation:
ama: Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:10.15479/at:ista:18443
apa: Sisak, M. A. (2024). T-dual branes on hyperkähler manifolds. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:18443
chicago: Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18443.
ieee: M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science
and Technology Austria, 2024.
ista: Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science
and Technology Austria.
mla: Sisak, Maria A. T-Dual Branes on Hyperkähler Manifolds. Institute of
Science and Technology Austria, 2024, doi:10.15479/at:ista:18443.
short: M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-10-19T12:00:37Z
date_published: 2024-10-24T00:00:00Z
date_updated: 2026-10-02T11:43:57Z
day: '24'
ddc:
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TaHa
doi: 10.15479/at:ista:18443
doi_confirm: '1'
file:
- access_level: open_access
checksum: 8c4893e726aaa4b3efb82758da9b6851
content_type: application/pdf
creator: msisak
date_created: 2024-10-23T14:42:45Z
date_updated: 2024-10-23T14:42:45Z
file_id: '18467'
file_name: MASisak_dissertation.pdf
file_size: 1672547
relation: main_file
success: 1
- access_level: closed
checksum: 1831b072e861a1e5481024ca9d02b036
content_type: application/x-zip-compressed
creator: msisak
date_created: 2024-10-23T14:43:56Z
date_updated: 2024-10-24T08:09:13Z
file_id: '18468'
file_name: MASisak_source.zip
file_size: 617913
relation: source_file
file_date_updated: 2024-10-24T08:09:13Z
fulldoi: https://doi.org/10.15479/at:ista:18443
has_accepted_license: '1'
keyword:
- hyperkaehler geometry
- branes
- mirror symmetry
- T-duality
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '178'
project:
- _id: 6286e8c4-2b32-11ec-9570-f5297902f67f
grant_number: '26069'
name: Branes on hyperkähler manifolds
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
researchdata_availability: no
status: public
supervisor:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
supplementarymaterial: no
title: T-dual branes on hyperkähler manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...