---
_id: '17456'
abstract:
- lang: eng
text: "Data-parallel distributed training of deep neural networks (DNN) has gained
very widespread adoption, but can still experience communication bottlenecks.
To address this issue, entire families of compression mechanisms have been developed,
including quantization, sparsification, and low-rank approximation, some of which
are seeing significant practical adoption. Despite this progress, almost all known
compression schemes apply compression uniformly across DNN layers, although layers
are heterogeneous in terms of parameter count and their impact on model accuracy.In
this work, we provide a general framework for adapting the degree of compression
across the model's layers dynamically during training, improving the overall compression,
while leading to substantial speedups, without sacrificing accuracy. Our framework,
called L-GreCo, is based on an adaptive algorithm, which automatically picks the
optimal compression parameters for model layers guaranteeing the best compression
ratio while satisfying an error constraint. Extensive experiments over image classification
and language modeling tasks shows that L-GreCo is effective across all existing
families of compression methods, and achieves up to 2.5\r\n×\r\n training speedup
and up to 5\r\n×\r\n compression improvement over efficient implementations of
existing approaches, while recovering full accuracy. Moreover, L-GreCo is complementary
to existing adaptive algorithms, improving their compression ratio by 50\\% and
practical throughput by 66\\%. An anonymized implementation is available at https://github.com/LGrCo/L-GreCo."
article_processing_charge: No
arxiv: 1
author:
- first_name: Ilia
full_name: Markov, Ilia
id: D0CF4148-C985-11E9-8066-0BDEE5697425
last_name: Markov
- first_name: Kaveh
full_name: Alimohammadi, Kaveh
last_name: Alimohammadi
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Markov I, Alimohammadi K, Frantar E, Alistarh D-A. L-GreCo: Layerwise-adaptive
gradient compression for efficient data-parallel deep learning. In: Gibbons P,
Pekhimenko G, De Sa C, eds. Proceedings of Machine Learning and Systems .
Vol 6. Association for Computing Machinery; 2024.'
apa: 'Markov, I., Alimohammadi, K., Frantar, E., & Alistarh, D.-A. (2024). L-GreCo:
Layerwise-adaptive gradient compression for efficient data-parallel deep learning.
In P. Gibbons, G. Pekhimenko, & C. De Sa (Eds.), Proceedings of Machine
Learning and Systems (Vol. 6). Athens, Greece: Association for Computing
Machinery.'
chicago: 'Markov, Ilia, Kaveh Alimohammadi, Elias Frantar, and Dan-Adrian Alistarh.
“L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel
Deep Learning.” In Proceedings of Machine Learning and Systems , edited
by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6. Association for Computing
Machinery, 2024.'
ieee: 'I. Markov, K. Alimohammadi, E. Frantar, and D.-A. Alistarh, “L-GreCo: Layerwise-adaptive
gradient compression for efficient data-parallel deep learning,” in Proceedings
of Machine Learning and Systems , Athens, Greece, 2024, vol. 6.'
ista: 'Markov I, Alimohammadi K, Frantar E, Alistarh D-A. 2024. L-GreCo: Layerwise-adaptive
gradient compression for efficient data-parallel deep learning. Proceedings of
Machine Learning and Systems . MLSys: Machine Learning and Systems vol. 6.'
mla: 'Markov, Ilia, et al. “L-GreCo: Layerwise-Adaptive Gradient Compression for
Efficient Data-Parallel Deep Learning.” Proceedings of Machine Learning and
Systems , edited by P. Gibbons et al., vol. 6, Association for Computing Machinery,
2024.'
short: I. Markov, K. Alimohammadi, E. Frantar, D.-A. Alistarh, in:, P. Gibbons,
G. Pekhimenko, C. De Sa (Eds.), Proceedings of Machine Learning and Systems ,
Association for Computing Machinery, 2024.
conference:
end_date: 2024-04-22
location: Athens, Greece
name: 'MLSys: Machine Learning and Systems'
start_date: 2024-04-22
corr_author: '1'
das_tickbox: '0'
date_created: 2024-08-22T08:29:25Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-02T11:20:05Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
editor:
- first_name: P.
full_name: Gibbons, P.
last_name: Gibbons
- first_name: G.
full_name: Pekhimenko, G.
last_name: Pekhimenko
- first_name: C.
full_name: De Sa, C.
last_name: De Sa
external_id:
arxiv:
- '2210.17357'
intvolume: ' 6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.mlsys.org/paper_files/paper/2024/hash/9069a8976ff06f6443e7f4172990a580-Abstract-Conference.html
month: '04'
oa: 1
oa_version: Published Version
publication: 'Proceedings of Machine Learning and Systems '
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '17490'
relation: dissertation_contains
status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: 'L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel
deep learning'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2024'
...
---
OA_place: publisher
_id: '18766'
abstract:
- lang: eng
text: Poxviruses are large pleomorphic double-stranded DNA viruses that include
well known members such as variola virus, the causative agent of smallpox, Mpox
virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain
for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic
DNA viruses in general and poxviruses specifically, as many features, such as
core morphology and structural proteins, are well conserved within this family.
Despite decades of research, our understanding of the structural components and
proteins that comprise the poxvirus core in mature virions remains limited. Although
major core proteins were identified via indirect experimental evidence, the core's
complexity, with its large size, structure and number of involved proteins, has
hindered efforts to achieve high-resolution insights and to define the roles of
the individual proteins. The specific protein composition of the core's individual
layers, including the palisade layer and the inner core wall, has remained unclear.
In this study, we have merged multiple approaches, including single particle cryo
electron microscopy of purified virus cores, cryo-electron tomography and subtomogram
averaging of mature virions and molecular modeling to elucidate the structural
determinants of the VACV core. Due to the lack of experimentally derived structures,
either in situ or reconstituted in vitro, we used Alphafold to predict models
of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results
show that the VACV core is composed of several layers with varying local symmetries,
forming more intricate interactions than observed previously. This allowed us
to identify several molecular building blocks forming the viral core lattice.
In particular, we identified trimers of protein A10 as a major core structure
that forms the palisade layer of the viral core. Additionally, we revealed that
six petals of a flower shaped core pore within the core wall are composed of A10
trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that
could potentially accommodate an A3 dimer. Integrating descriptions of protein
interactions from previous studies enabled us to provide a detailed structural
model of the poxvirus core wall, and our findings indicate that the interactions
within A10 trimers are likely consistent across orthopox- and parapoxviruses.
This combined application of cryo-SPA and cryo-ET can help overcome obstacles
in studying complex virus structures in the future, including their key assembly
proteins, interactions, and the formation into a core lattice. Our work provides
important fundamental new insights into poxvirus core architecture, also considering
the recent re-emergence of poxviruses.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: "This work was funded by the Austrian Science Fund (FWF) grant P31445
and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units,
particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and
the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially
thank Alois for assisting me with the\r\ninstallation of countless new software
and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for
his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving
the process to ensure that I obtained the best possible\r\ndata from my sample."
alternative_title:
- ISTA thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
citation:
ama: Datler J. Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766
apa: Datler, J. (2024). Elucidating the structural determinants of the poxvirus
core using multi-modal cryo-EM. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18766
chicago: Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus
Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria,
2024. https://doi.org/10.15479/at:ista:18766.
ieee: J. Datler, “Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.
ista: Datler J. 2024. Elucidating the structural determinants of the poxvirus core
using multi-modal cryo-EM. Institute of Science and Technology Austria.
mla: Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core
Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024,
doi:10.15479/at:ista:18766.
short: J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using
Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '1'
date_created: 2025-01-07T10:23:12Z
date_published: 2024-12-30T00:00:00Z
date_updated: 2026-10-02T11:21:19Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:18766
doi_confirm: '1'
file:
- access_level: closed
checksum: 3e51cab327c754045c3d29c1a50cc9a9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jstanger
date_created: 2025-01-07T12:15:11Z
date_updated: 2025-01-07T12:15:11Z
file_id: '18769'
file_name: PhD_thesis_Julia_Datler.docx
file_size: 38814932
relation: source_file
- access_level: open_access
checksum: 22fabe5b97950bf852212f6edb555173
content_type: application/pdf
creator: jstanger
date_created: 2025-01-07T12:15:14Z
date_updated: 2025-01-07T12:15:14Z
file_id: '18770'
file_name: PhD_thesis_Julia_Datler.pdf
file_size: 12044865
relation: main_file
success: 1
file_date_updated: 2025-01-07T12:15:14Z
fulldoi: https://doi.org/10.15479/at:ista:18766
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- cryo-SPA
- Structural Virology
- Poxvirus
- Vaccinia Virus
- Structural Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: '106'
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication_identifier:
isbn:
- 978-3-99078-049-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: part_of_dissertation
status: public
- id: '14979'
relation: part_of_dissertation
status: public
researchdata_availability: yes
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
supplementarymaterial: no
title: Elucidating the structural determinants of the poxvirus core using multi-modal
cryo-EM
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'
...
---
APC_amount: 11700 EUR
OA_place: publisher
OA_type: hybrid
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "The electron microscopy density maps of the A10 trimer
and the hexameric flower-shaped pore, the subtomogram average of the palisade layer
and representative tomograms for complete viruses as well as isolated cores have
been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410,
EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model
of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB
8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction
are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein
IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox
virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1),
orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and
Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1)
were used for protein sequence alignment. Source data for MS experiments are provided
as Supplementary Information accompanying this manuscript."
date_created: 2024-02-12T09:59:45Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T11:21:19Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
isi:
- '001158144600002'
pmid:
- '38316877'
file:
- access_level: open_access
checksum: bda7bf65d81455480efaed8ca293b0db
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:27:22Z
date_updated: 2024-07-22T11:27:22Z
file_id: '17307'
file_name: 2024_NatureStrucBio_Datler.pdf
file_size: 17485494
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:27:22Z
fulldoi: https://doi.org/10.1038/s41594-023-01201-6
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1114-1123
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
record:
- id: '18766'
relation: dissertation_contains
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
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: 31
year: '2024'
...
---
OA_place: publisher
_id: '17850'
abstract:
- lang: eng
text: "Understanding the relationship between a given phenotype and its underlying
genotype or genotypes is one of the most pressing challenges of biology, as it
lies at the heart of not only basic understanding of evolutionary theory, but
also of practical applications in medicine and bioengineering. Understanding this
relationship is complicated by the ubiquitous phenomenon of epistasis, wherein
mutation effects are dependent on their genetic context. Fitness landscapes —
representations of phenotype as a function of genotype — are being increasingly
used as a tool to study the effects and interactions of thousands of mutations,
but are experimentally limited to exploring a small fraction of a protein’s theoretical
sequence space. Furthermore, not all regions of said sequence space are necessarily
equally informative. Thus, gene selection for landscape surveys should be carefully
considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn
this work, we analyzed the fitness landscapes of orthologous green fluorescent
proteins from four different species, by systematically measuring the phenotype,
fluorescence, of tens of thousands of mutant genotypes from each protein. These
landscapes were highly heterogeneous, with some genes being mutationally robust
and displaying epistasis only rarely, and others being highly epistatic and mutationally
fragile. We used this data to train machine learning models to predict fluorescence
from genotype. Although the training data contained almost exclusively genotypes
with less than 3% sequence divergence from the original wild-type sequences, we
were able to create novel, functional genotypes with up to 20% sequence divergence.
Counterintuitively however, genes with high mutational robustness and rare epistasis
were more difficult to introduce large numbers of mutations into, not less. This
represents the first study of large-scale fitness landscapes of a protein family,
and provides insights into how to approach future landscape surveys and their
applications in novel protein design."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
citation:
ama: Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent
proteins. 2024. doi:10.15479/at:ista:17850
apa: Gonzalez Somermeyer, L. (2024). Fitness landscapes of orthologous green
fluorescent proteins. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17850
chicago: Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent
Proteins.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17850.
ieee: L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent
proteins,” Institute of Science and Technology Austria, 2024.
ista: Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent
proteins. Institute of Science and Technology Austria.
mla: Gonzalez Somermeyer, Louisa. Fitness Landscapes of Orthologous Green Fluorescent
Proteins. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17850.
short: L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent
Proteins, Institute of Science and Technology Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-06T12:57:44Z
date_published: 2024-09-06T00:00:00Z
date_updated: 2026-10-02T11:21:41Z
day: '06'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FyKo
doi: 10.15479/at:ista:17850
doi_confirm: '1'
ec_funded: 1
file:
- access_level: open_access
checksum: d3303724e8d3c91321d71bbad4062048
content_type: application/pdf
creator: lgonzale
date_created: 2024-09-27T10:32:33Z
date_updated: 2024-09-27T10:32:33Z
file_id: '18151'
file_name: louisa_thesis_draft__240904b.pdf
file_size: 11219837
relation: main_file
- access_level: closed
checksum: 22e63f7f9014dffde2af7a47e7d1d014
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lgonzale
date_created: 2024-09-27T10:34:34Z
date_updated: 2024-09-27T10:34:34Z
file_id: '18152'
file_name: louisa_thesis_draft__240904b.docx
file_size: 43338677
relation: source_file
file_date_updated: 2024-09-27T10:34:34Z
fulldoi: https://doi.org/10.15479/at:ista:17850
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '89'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: software
url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks
record:
- id: '11448'
relation: part_of_dissertation
status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
supplementarymaterial: no
title: Fitness landscapes of orthologous green fluorescent proteins
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'
...
---
_id: '14901'
abstract:
- lang: eng
text: Global services like navigation, communication, and Earth observation have
increased dramatically in the 21st century due to advances in outer space industries.
But as orbits become increasingly crowded with both satellites and inevitable
space debris pollution, continued operations become endangered by the heightened
risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical
threshold of orbiting debris triggers a runaway positive feedback loop of debris
collisions, creating debris congestion that can render orbits unusable. As this
potential tipping point becomes more widely recognized, there have been renewed
calls for debris mitigation and removal. Here, we combine complex systems and
social-ecological systems approaches to study how these efforts may affect space
debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically,
we model how debris levels are affected by future launch rates, cleanup activities,
and collisions between extant debris. We contextualize and interpret our dynamic
model within a discussion of existing space debris governance and other social,
economic, and geopolitical factors that may influence effective collective management
of the orbital commons. In line with previous studies, our model finds that debris
congestion may be reached in less than 200 years, though a holistic management
strategy combining removal and mitigation actions can avoid such outcomes while
continuing space activities. Moreover, although active debris removal may be particularly
effective, the current lack of market and governance support may impede its implementation.
Research into these critical dynamics and the multi-faceted variables that influence
debris outcomes can support policymakers in curating impactful governance strategies
and realistic transition pathways to sustaining debris-free orbits. Overall, our
study is useful for communicating about space debris sustainability in policy
and education settings by providing an exploration of policy portfolio options
supported by a simple and clear social-ecological modeling approach.
acknowledgement: The authors would like to thank the special issue co-editors, Marco
Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped
improve the manuscript. The paper also benefited from suggestions by other author
participants in this special issue. We would also like to thank the 2022 Santa Fe
Institute Complex Systems Summer School for providing space to initiate this study.
article_processing_charge: Yes
article_type: original
author:
- first_name: Keiko
full_name: Nomura, Keiko
last_name: Nomura
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Haily
full_name: Merritt, Haily
last_name: Merritt
- first_name: Mathieu
full_name: Baltussen, Mathieu
last_name: Baltussen
- first_name: Darcy
full_name: Bird, Darcy
last_name: Bird
- first_name: Annika
full_name: Tjuka, Annika
last_name: Tjuka
- first_name: Dan
full_name: Falk, Dan
last_name: Falk
citation:
ama: Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low
earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275
apa: Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &
Falk, D. (2024). Tipping points of space debris in low earth orbit. International
Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275
chicago: Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird,
Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.”
International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.
ieee: K. Nomura et al., “Tipping points of space debris in low earth orbit,”
International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.
ista: Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024.
Tipping points of space debris in low earth orbit. International Journal of the
Commons. 18(1).
mla: Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.”
International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024,
doi:10.5334/ijc.1275.
short: K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk,
International Journal of the Commons 18 (2024).
das_tickbox: '0'
date_created: 2024-01-30T11:58:02Z
date_published: 2024-01-11T00:00:00Z
date_updated: 2026-10-02T11:22:03Z
day: '11'
ddc:
- '550'
department:
- _id: GradSch
- _id: GaTk
doi: 10.5334/ijc.1275
file:
- access_level: open_access
checksum: b80ebc889033c365d8f8c05a0c655382
content_type: application/pdf
creator: dernst
date_created: 2024-02-05T10:06:35Z
date_updated: 2024-02-05T10:06:35Z
file_id: '14939'
file_name: 2023_IntJourCommons_Nomura.pdf
file_size: 1305786
relation: main_file
success: 1
file_date_updated: 2024-02-05T10:06:35Z
fulldoi: https://doi.org/10.5334/ijc.1275
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
keyword:
- Sociology and Political Science
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: International Journal of the Commons
publication_identifier:
issn:
- 1875-0281
publication_status: published
publisher: Ubiquity Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Tipping points of space debris in low earth orbit
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: 18
year: '2024'
...
---
OA_place: publisher
_id: '18076'
abstract:
- lang: eng
text: "The new era of Ge has opened up new possibilities in quantum computing. The
maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor
Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons)
employing semiconductor Josephson\r\njunctions have recently emerged as building
blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon
fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional
hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor
from the Ge quantum well. The Josephson junction is then integrated\r\ninto an
Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe
qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain
characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults,
combined with the recent advances in the spin qubit field, pave the way towards
novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
citation:
ama: Sagi O. Hybrid circuits on planar Germanium. 2024. doi:10.15479/at:ista:18076
apa: Sagi, O. (2024). Hybrid circuits on planar Germanium. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:18076
chicago: Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science
and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18076.
ieee: O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology
Austria, 2024.
ista: Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and
Technology Austria.
mla: Sagi, Oliver. Hybrid Circuits on Planar Germanium. Institute of Science
and Technology Austria, 2024, doi:10.15479/at:ista:18076.
short: O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology
Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-16T12:58:36Z
date_published: 2024-09-18T00:00:00Z
date_updated: 2026-10-02T11:22:29Z
day: '18'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:18076
doi_confirm: '1'
ec_funded: 1
file:
- access_level: open_access
checksum: d01d0e2846c2f3ac5bb14d321554a4cd
content_type: application/pdf
creator: osagi
date_created: 2024-09-18T14:13:01Z
date_updated: 2024-09-18T14:13:01Z
file_id: '18093'
file_name: OliverSagi_Thesis_pdfa.pdf
file_size: 86679095
relation: main_file
success: 1
- access_level: local
checksum: 0543f473d509ee545f4ed3a56f742f4b
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-09-18T14:14:02Z
date_updated: 2024-09-19T09:20:33Z
file_id: '18094'
file_name: Thesis_OliverSagi.zip
file_size: 172098524
relation: source_file
file_date_updated: 2024-09-19T09:20:33Z
fulldoi: https://doi.org/10.15479/at:ista:18076
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '111'
project:
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17202'
relation: part_of_dissertation
status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
supplementarymaterial: yes
title: Hybrid circuits on planar Germanium
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17170'
abstract:
- lang: eng
text: "In this article we extend and strengthen the seminal work by Niyogi, Smale,
and Weinberger on the learning of the homotopy type from a sample of an underlying
space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds
with positive reach embedded in ℝ^d. We extend their results in the following
ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with
lower bounded sectional curvature. - In both types of ambient spaces, we study
sets of positive reach - a significantly more general setting than C² manifolds
- as well as general manifolds of positive reach. - The sample P of a set (or
a manifold) \U0001D4AE of positive reach may be noisy. We work with two one-sided
Hausdorff distances - ε and δ - between P and \U0001D4AE. We provide tight bounds
in terms of ε and δ, that guarantee that there exists a parameter r such that
the union of balls of radius r centred at the sample P deformation-retracts to
\U0001D4AE. We exhibit their tightness by an explicit construction. We carefully
distinguish the roles of δ and ε. This is not only essential to achieve tight
bounds, but also sensible in practical situations, since it allows one to adapt
the bound according to sample density and the amount of noise present in the sample
separately."
acknowledgement: "This research has been supported by the European Research Council
(ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF),
grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian
Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant
No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur."
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Hana
full_name: Kourimska, Hana
id: D9B8E14C-3C26-11EA-98F5-1F833DDC885E
last_name: Kourimska
orcid: 0000-0001-7841-0091
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
- first_name: Ishika
full_name: Ghosh, Ishika
id: ee449b28-344d-11ef-a6d5-9ca430e9e9ff
last_name: Ghosh
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of
homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and
of Riemannian manifolds. In: 40th International Symposium on Computational
Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19.
doi:10.4230/LIPIcs.SoCG.2024.11'
apa: 'Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson,
E. R., & Wintraecken, M. (2024). Tight bounds for the learning of homotopy
à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian
manifolds. In 40th International Symposium on Computational Geometry (Vol.
293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SoCG.2024.11'
chicago: Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh,
André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds
for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of
Euclidean Spaces and of Riemannian Manifolds.” In 40th International Symposium
on Computational Geometry, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.11.
ieee: D. Attali et al., “Tight bounds for the learning of homotopy à la Niyogi,
Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,”
in 40th International Symposium on Computational Geometry, Athens, Greece,
2024, vol. 293, p. 11:1-11:19.
ista: 'Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken
M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger
for subsets of euclidean spaces and of Riemannian manifolds. 40th International
Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry,
LIPIcs, vol. 293, 11:1-11:19.'
mla: Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi,
Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.”
40th International Symposium on Computational Geometry, vol. 293, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:10.4230/LIPIcs.SoCG.2024.11.
short: D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson,
M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.
conference:
end_date: 2024-06-14
location: Athens, Greece
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2024-06-11
das_tickbox: '0'
date_created: 2024-06-25T11:45:58Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2026-10-02T11:23:43Z
day: '06'
ddc:
- '516'
department:
- _id: GradSch
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2024.11
ec_funded: 1
external_id:
arxiv:
- '2206.10485'
file:
- access_level: open_access
checksum: 6a2ddc8b51aa58f197a8b294750f1f8d
content_type: application/pdf
creator: cfillmor
date_created: 2024-06-25T11:47:26Z
date_updated: 2024-06-25T11:47:26Z
file_id: '17171'
file_name: LIPIcs.SoCG.2024.11.pdf
file_size: 20886142
relation: main_file
success: 1
file_date_updated: 2024-06-25T11:47:26Z
fulldoi: https://doi.org/10.4230/LIPIcs.SoCG.2024.11
has_accepted_license: '1'
intvolume: ' 293'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 11:1-11:19
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
publication: 40th International Symposium on Computational Geometry
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959773164'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger
for subsets of euclidean spaces and of Riemannian 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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 293
year: '2024'
...
---
APC_amount: 6828 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17202'
abstract:
- lang: eng
text: Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions
have recently emerged as building blocks for hybrid quantum circuits. In this
study, we present a gatemon fabricated in planar Germanium. We induce superconductivity
in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which
separates the superconductor from the Ge quantum well. The Josephson junction
is then integrated into an Xmon circuit and capacitively coupled to a transmission
line resonator. We showcase the qubit tunability in a broad frequency range with
resonator and two-tone spectroscopy. Time-domain characterizations reveal energy
relaxation and coherence times up to 75 ns. Our results, combined with the recent
advances in the spin qubit field, pave the way towards novel hybrid and protected
qubits in a group IV, CMOS-compatible material.
acknowledged_ssus:
- _id: ScienComp
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten
Kjaergard and Javad Shabani for their valuable insights and comments. This research
was supported by the Scientific Service Units of ISTA through resources provided
by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and
related results were made possible with the support of the NOMIS Foundation and
the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge
the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial
support."
article_number: '6400'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Alessandro
full_name: Crippa, Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Levon
full_name: Baghumyan, Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- first_name: Giorgio
full_name: Fabris, Giorgio
id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352
last_name: Fabris
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar
Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6
apa: Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G.,
… Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-50763-6
chicago: Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan,
Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar
Ge.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6.
ieee: O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature
Communications, vol. 15. Springer Nature, 2024.
ista: Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani
F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable
transmon qubit in planar Ge. Nature Communications. 15, 6400.
mla: Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature
Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6.
short: O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor,
F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature
Communications 15 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All experimental data included in this work will be available
at the ISTA Research Data Repository
date_created: 2024-07-04T11:40:45Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-10-02T11:23:23Z
day: '30'
ddc:
- '530'
department:
- _id: GeKa
- _id: JoFi
- _id: GradSch
doi: 10.1038/s41467-024-50763-6
external_id:
arxiv:
- '2403.16774'
isi:
- '001281271000022'
pmid:
- '39080279'
file:
- access_level: open_access
checksum: ddf5361dcb6c543e2cea818501c09910
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:38:01Z
date_updated: 2024-08-05T08:38:01Z
file_id: '17388'
file_name: 2024_NatureComm_Sagi.pdf
file_size: 1928001
relation: main_file
success: 1
file_date_updated: 2024-08-05T08:38:01Z
fulldoi: https://doi.org/10.1038/s41467-024-50763-6
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-024-53910-1
record:
- id: '18076'
relation: dissertation_contains
status: public
- id: '17196'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A gate tunable transmon qubit in planar Ge
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: 15
year: '2024'
...
---
_id: '17196'
abstract:
- lang: eng
text: This .zip File contains the data for the figures presented in the main text
and supplementary material of "A gate tunable transmon qubit in planar Ge" by
O.Sagi et al. The measurements were done using Qcodes. The description of the
files and the instructions on opening the data can be found in the Readme. An
additional Jupyter Notebook is attached that walks through the data analysis.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'This research was supported by the Scientific Service Units of ISTA
through resources provided by the MIBA Machine Shop and the Nanofabrication facility. '
article_processing_charge: No
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
citation:
ama: Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:10.15479/AT:ISTA:17196
apa: Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:17196
chicago: Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science
and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17196.
ieee: O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and
Technology Austria, 2024.
ista: Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:17196.
mla: Sagi, Oliver. A Gate-Tunable Transmon in Planar Ge. Institute of Science
and Technology Austria, 2024, doi:10.15479/AT:ISTA:17196.
short: O. Sagi, (2024).
contributor:
- contributor_type: project_member
first_name: Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- contributor_type: project_member
first_name: Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- contributor_type: project_member
first_name: Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
- contributor_type: project_member
first_name: Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- contributor_type: project_member
first_name: Giorgio
id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352
last_name: Fabris
- contributor_type: project_member
first_name: Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
- contributor_type: project_member
first_name: Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- contributor_type: project_member
first_name: Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- contributor_type: project_member
first_name: Stefano
last_name: Calcaterra
- contributor_type: project_member
first_name: Daniel
last_name: Chrastina
- contributor_type: project_member
first_name: Giovanni
last_name: Isella
- contributor_type: supervisor
first_name: Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
corr_author: '1'
date_created: 2024-07-04T10:14:34Z
date_published: 2024-07-04T00:00:00Z
date_updated: 2026-10-02T11:23:23Z
day: '04'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
- _id: JoFi
doi: 10.15479/AT:ISTA:17196
doi_confirm: '1'
file:
- access_level: open_access
checksum: a9f640a0b72a92171353f3ea14406f0b
content_type: application/octet-stream
creator: osagi
date_created: 2024-07-04T10:01:51Z
date_updated: 2024-07-04T10:01:51Z
file_id: '17197'
file_name: GeGatemon_DataAnalysis.ipynb
file_size: 1960182
relation: main_file
success: 1
- access_level: open_access
checksum: f0feec931233e8e845ade56165c1588f
content_type: application/vnd.openxmlformats-officedocument.presentationml.presentation
creator: osagi
date_created: 2024-07-04T10:01:50Z
date_updated: 2024-07-04T10:01:50Z
file_id: '17198'
file_name: OlSa_Readme.pptx
file_size: 34194
relation: main_file
success: 1
- access_level: open_access
checksum: 92bb11e3a508d736d01ff0738a1172c7
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:16Z
date_updated: 2024-07-04T10:11:16Z
file_id: '17199'
file_name: Al_Transmon.zip
file_size: 72939292
relation: main_file
success: 1
- access_level: open_access
checksum: 871e96fe0ecc97581196e883045cd516
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:40Z
date_updated: 2024-07-04T10:11:40Z
file_id: '17200'
file_name: Gatemon_RT_5nm_1.zip
file_size: 465618029
relation: main_file
success: 1
- access_level: open_access
checksum: a3e141af90f0104b7269c8a72370848a
content_type: application/x-zip-compressed
creator: osagi
date_created: 2024-07-04T10:11:35Z
date_updated: 2024-07-04T10:11:35Z
file_id: '17201'
file_name: Gatemon_RT_5nm_2.zip
file_size: 281503513
relation: main_file
success: 1
file_date_updated: 2024-07-04T10:11:40Z
fulldoi: https://doi.org/10.15479/AT:ISTA:17196
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17202'
relation: used_in_publication
status: public
status: public
title: A gate-tunable transmon in planar Ge
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17141'
abstract:
- lang: eng
text: The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted
to (de)active transcriptional regulation, thus controlling auxin-associated developmental
processes. However, the theme of a rapid auxin response has emerged since the
2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling
components have been identified to mediate both slow and rapid auxin responses,
which unveils the complexity of auxin signaling.
acknowledgement: "We thank other lab members for their critical comments on this manuscript.
We also thank the editor and reviewers for their constructive comments to improve
our manuscript. We apologize to authors whose important work we could not include
due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural
University (9232308314) and the Science and Technology Department of Jiangxi Province
(20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province
(20202ACB215002) to SYP."
article_number: erae246
article_processing_charge: No
article_type: original
author:
- first_name: Zilin
full_name: Zhang, Zilin
last_name: Zhang
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Shuaiying
full_name: Peng, Shuaiying
last_name: Peng
- first_name: Huibin
full_name: Han, Huibin
last_name: Han
citation:
ama: Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis.
Journal of Experimental Botany. 2024;75(18). doi:10.1093/jxb/erae246
apa: Zhang, Z., Chen, H., Peng, S., & Han, H. (2024). Slow and rapid auxin responses
in Arabidopsis. Journal of Experimental Botany. Oxford University Press.
https://doi.org/10.1093/jxb/erae246
chicago: Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and
Rapid Auxin Responses in Arabidopsis.” Journal of Experimental Botany.
Oxford University Press, 2024. https://doi.org/10.1093/jxb/erae246.
ieee: Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in
Arabidopsis,” Journal of Experimental Botany, vol. 75, no. 18. Oxford University
Press, 2024.
ista: Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis.
Journal of Experimental Botany. 75(18), erae246.
mla: Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” Journal
of Experimental Botany, vol. 75, no. 18, erae246, Oxford University Press,
2024, doi:10.1093/jxb/erae246.
short: Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024).
das_tickbox: '0'
date_created: 2024-06-15T19:50:15Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2026-10-02T11:25:38Z
day: '27'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
doi: 10.1093/jxb/erae246
external_id:
isi:
- '001270051200001'
pmid:
- '38794966'
file:
- access_level: open_access
checksum: 91b9435ed0f6640809c7588df19abf2f
content_type: application/pdf
creator: dernst
date_created: 2025-01-02T10:26:22Z
date_updated: 2025-01-02T10:26:22Z
file_id: '18720'
file_name: 2024_JourExperimentalBotany_Zhang.pdf
file_size: 763097
relation: main_file
success: 1
file_date_updated: 2025-01-02T10:26:22Z
fulldoi: https://doi.org/10.1093/jxb/erae246
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
issn:
- 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Slow and rapid auxin responses in Arabidopsis
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: 75
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
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
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:
record:
- id: '19003'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: Super-resolution expansion microscopy in plant roots
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
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'
file:
- access_level: closed
checksum: b61651d417cafddd740a8528f46068c5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mtavakol
date_created: 2024-12-20T10:23:17Z
date_updated: 2024-12-20T10:31:37Z
file_id: '18699'
file_name: Thesis_Mojtaba Tavakoli_.docx
file_size: 118593521
relation: source_file
- access_level: closed
checksum: c80bcfd1a34c23afc3538052325283e5
content_type: application/pdf
creator: mtavakol
date_created: 2024-12-20T10:25:12Z
date_updated: 2026-07-28T08:33:51Z
embargo: 2027-08-01
embargo_to: open_access
file_id: '18700'
file_name: Thesis_Mojtaba Tavakoli_.pdf
file_size: 63885521
relation: main_file
file_date_updated: 2026-07-28T08:33:51Z
fulldoi: https://doi.org/10.15479/at:ista:18681
has_accepted_license: '1'
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: 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
date_updated: 2026-10-02T11:34:35Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: MaMo
- _id: ChLa
external_id:
arxiv:
- '2405.14468'
file:
- access_level: open_access
checksum: b7b79f1ea3ac1e9e11b3d91faaeb0780
content_type: application/pdf
creator: dernst
date_created: 2025-02-04T08:11:25Z
date_updated: 2025-02-04T08:11:25Z
file_id: '18989'
file_name: 2024_NeurIPS_Sukenik.pdf
file_size: 1784118
relation: main_file
success: 1
file_date_updated: 2025-02-04T08:11:25Z
has_accepted_license: '1'
intvolume: ' 37'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
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'
...
---
OA_place: publisher
OA_type: gold
_id: '18515'
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:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:18515
doi_confirm: '1'
file:
- access_level: open_access
checksum: c32cf7bc75748d9c551d8eb70178bbec
content_type: application/pdf
creator: psurendr
date_created: 2024-11-07T10:59:29Z
date_updated: 2024-11-07T10:59:29Z
file_id: '18519'
file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf
file_size: 37019760
relation: main_file
success: 1
- access_level: closed
checksum: 4417e02d54084d89e75734e18caaa96d
content_type: application/zip
creator: psurendr
date_created: 2024-11-07T10:59:42Z
date_updated: 2024-11-07T10:59:42Z
file_id: '18520'
file_name: PhD Thesis- Parvathy_071124.zip
file_size: 41198857
relation: source_file
file_date_updated: 2024-11-07T10:59:42Z
fulldoi: https://doi.org/10.15479/at:ista:18515
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '219'
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _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
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
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'
...
---
APC_amount: 3028,31 EUR
DOAJ_listed: '1'
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'
file:
- access_level: open_access
checksum: 8f744d94956a1683b473b1cf9b411a37
content_type: application/pdf
creator: dernst
date_created: 2024-09-23T09:46:20Z
date_updated: 2024-09-23T09:46:20Z
file_id: '18125'
file_name: 2024_PhysicalReviewResearch_Maslov.pdf
file_size: 1563824
relation: main_file
success: 1
file_date_updated: 2024-09-23T09:46:20Z
fulldoi: https://doi.org/10.1103/physrevresearch.6.033277
has_accepted_license: '1'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
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'
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '19048'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Theory of angular momentum transfer from light to molecules
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: 6
year: '2024'
...