---
_id: '13316'
abstract:
- lang: eng
text: Although budding yeast has been extensively used as a model organism for studying
organelle functions and intracellular vesicle trafficking, whether it possesses
an independent endocytic early/sorting compartment that sorts endocytic cargos
to the endo-lysosomal pathway or the recycling pathway has long been unclear.
The structure and properties of the endocytic early/sorting compartment differ
significantly between organisms; in plant cells, the trans-Golgi network (TGN)
serves this role, whereas in mammalian cells a separate intracellular structure
performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to
the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic
vesicles, but which compartment is the direct target for endocytic vesicles remained
unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of
fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within
the TGN functions as the early/sorting compartment. After arriving here, endocytic
cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing
endosomal compartment through the pathway requiring the clathrin adaptors GGAs.
Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment,
and the deletion of GGAs has little effect on another TGN region where Sec7p is
present but suppresses dynamics of the Tlg2-residing early/sorting compartment,
indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in
the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting
compartment and function independently of the Sec7p-residing region within the
TGN.
acknowledgement: 'This work was supported by JSPS KAKENHI grant #18K062291, and the
Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the
Takeda Science Foundation, and Life Science Foundation of Japan to JT.'
article_number: e84850
article_processing_charge: Yes
article_type: original
author:
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Ayana
full_name: Tsukahara, Ayana
last_name: Tsukahara
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Takuro
full_name: Tojima, Takuro
last_name: Tojima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting
compartment exists as an independent sub-compartment within the trans-Golgi network.
eLife. 2023;12. doi:10.7554/eLife.84850
apa: Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano,
A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists
as an independent sub-compartment within the trans-Golgi network. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.84850
chicago: Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria
E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting
Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.”
ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850.
ieee: J. Y. Toshima et al., “The yeast endocytic early/sorting compartment
exists as an independent sub-compartment within the trans-Golgi network,” eLife,
vol. 12. eLife Sciences Publications, 2023.
ista: Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima
J. 2023. The yeast endocytic early/sorting compartment exists as an independent
sub-compartment within the trans-Golgi network. eLife. 12, e84850.
mla: Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists
as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife,
vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850.
short: J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano,
J. Toshima, ELife 12 (2023).
date_created: 2023-07-30T22:01:02Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2023-12-13T11:37:36Z
day: '21'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.84850
external_id:
isi:
- '001035372800001'
pmid:
- '37477116'
file:
- access_level: open_access
checksum: 2af111a00cf5e3a956f7f0fd13199b15
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:43:00Z
date_updated: 2023-07-31T07:43:00Z
file_id: '13324'
file_name: 2023_eLife_Toshima.pdf
file_size: 11980913
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:43:00Z
fulldoi: https://doi.org/10.7554/eLife.84850
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: The yeast endocytic early/sorting compartment exists as an independent sub-compartment
within the trans-Golgi network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '13319'
abstract:
- lang: eng
text: We prove that the generator of the L2 implementation of a KMS-symmetric quantum
Markov semigroup can be expressed as the square of a derivation with values in
a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially
symmetric semigroups and the second-named author for GNS-symmetric semigroups.
This result hinges on the introduction of a new completely positive map on the
algebra of bounded operators on the GNS Hilbert space. This transformation maps
symmetric Markov operators to symmetric Markov operators and is essential to obtain
the required inner product on the Hilbert bimodule.
acknowledgement: The authors are grateful to Martijn Caspers for helpful comments
on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi
grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator
algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit
Programme [ESP 156]. For the purpose of Open Access, the authors have applied a
CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising
from this submission. Open access funding provided by Austrian Science Fund (FWF).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Matthijs
full_name: Vernooij, Matthijs
last_name: Vernooij
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups.
Communications in Mathematical Physics. 2023;403:381-416. doi:10.1007/s00220-023-04795-6
apa: Vernooij, M., & Wirth, M. (2023). Derivations and KMS-symmetric quantum
Markov semigroups. Communications in Mathematical Physics. Springer Nature.
https://doi.org/10.1007/s00220-023-04795-6
chicago: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric
Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer
Nature, 2023. https://doi.org/10.1007/s00220-023-04795-6.
ieee: M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,”
Communications in Mathematical Physics, vol. 403. Springer Nature, pp.
381–416, 2023.
ista: Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups.
Communications in Mathematical Physics. 403, 381–416.
mla: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum
Markov Semigroups.” Communications in Mathematical Physics, vol. 403, Springer
Nature, 2023, pp. 381–416, doi:10.1007/s00220-023-04795-6.
short: M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023)
381–416.
corr_author: '1'
date_created: 2023-07-30T22:01:03Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-23T13:10:45Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00220-023-04795-6
external_id:
arxiv:
- '2303.15949'
isi:
- '001033655400002'
pmid:
- '37766789'
file:
- access_level: open_access
checksum: cca204e81891270216a0c84eb8bcd398
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:15:11Z
date_updated: 2024-01-30T12:15:11Z
file_id: '14905'
file_name: 2023_CommMathPhysics_Vernooij.pdf
file_size: 481209
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:15:11Z
fulldoi: https://doi.org/10.1007/s00220-023-04795-6
has_accepted_license: '1'
intvolume: ' 403'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 381-416
pmid: 1
project:
- _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833
grant_number: ESP156_N
name: Gradient flow techniques for quantum Markov semigroups
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivations and KMS-symmetric quantum Markov semigroups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 403
year: '2023'
...
---
OA_place: publisher
_id: '13331'
abstract:
- lang: eng
text: "The extension of extremal combinatorics to the setting of exterior algebra
is a work\r\nin progress that gained attention recently. In this thesis, we study
the combinatorial structure of exterior algebra by introducing a dictionary that
translates the notions from the set systems into the framework of exterior algebra.
We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner
theorem to the setting of exterior algebra in the simplest non-trivial case of
two-forms.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Seyda
full_name: Köse, Seyda
id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb
last_name: Köse
orcid: 0009-0008-0457-9730
citation:
ama: Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331
apa: Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13331
chicago: Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science
and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.
ieee: S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology
Austria, 2023.
ista: Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and
Technology Austria.
mla: Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science
and Technology Austria, 2023, doi:10.15479/at:ista:13331.
short: S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-07-31T10:20:55Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2026-04-07T13:29:29Z
day: '31'
ddc:
- '510'
- '516'
degree_awarded: MS
department:
- _id: GradSch
- _id: UlWa
doi: 10.15479/at:ista:13331
file:
- access_level: closed
checksum: 96ee518d796d02af71395622c45de03c
content_type: application/x-zip-compressed
creator: skoese
date_created: 2023-07-31T10:16:32Z
date_updated: 2023-07-31T10:16:32Z
file_id: '13333'
file_name: Exterior Algebra and Combinatorics.zip
file_size: 28684
relation: source_file
- access_level: open_access
checksum: f610f4713f88bc477de576aaa46b114e
content_type: application/pdf
creator: skoese
date_created: 2023-08-03T15:28:55Z
date_updated: 2023-08-03T15:28:55Z
file_id: '13480'
file_name: thesis-pdfa.pdf
file_size: 4953418
relation: main_file
success: 1
file_date_updated: 2023-08-03T15:28:55Z
fulldoi: https://doi.org/10.15479/at:ista:13331
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12680'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Exterior algebra and combinatorics
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '13336'
article_processing_charge: No
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
citation:
ama: 'Kleshnina M. kleshnina/stochgames_info: The effect of environmental information
on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564'
apa: 'Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental
information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564'
chicago: 'Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental
Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.'
ieee: 'M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information
on evolution of cooperation in stochastic games.” Zenodo, 2023.'
ista: 'Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental
information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.'
mla: 'Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental
Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023,
doi:10.5281/ZENODO.8059564.'
short: M. Kleshnina, (2023).
corr_author: '1'
date_created: 2023-07-31T11:30:46Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2025-04-15T06:54:58Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.5281/ZENODO.8059564
fulldoi: https://doi.org/10.5281/ZENODO.8059564
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8059564
month: '06'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '13258'
relation: used_in_publication
status: public
status: public
title: 'kleshnina/stochgames_info: The effect of environmental information on evolution
of cooperation in stochastic games'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13342'
abstract:
- lang: eng
text: Motile cells moving in multicellular organisms encounter microenvironments
of locally heterogeneous mechanochemical composition. Individual compositional
parameters like chemotactic signals, adhesiveness, and pore sizes are well known
to be sensed by motile cells, providing individual guidance cues for cellular
pathfinding. However, motile cells encounter diverse mechanochemical signals at
the same time, raising the question of how cells respond to locally diverse and
potentially competing signals on their migration routes. Here, we reveal that
motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for
adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using
mammalian immune cells and the amoebaDictyostelium discoideum,
we discover that frequent, rapid and long-distance nucleokinesis is a basic component
of amoeboid pathfinding, enabling cells to reorientate quickly between locally
competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch
and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the
‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired
nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment.
Our findings establish that nucleokinesis is required for amoeboid cell navigation.
Given that motile single-cell amoebae, many immune cells, and some cancer cells
utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis
underlies cellular navigation during unicellular biology, immunity, and disease.
acknowledgement: We thank Christoph Mayr and Bingzhi Wang for initial experiments
on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow
from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry,
EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte
Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of
the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry,
and the Animal Core Facility of the Biomedical Center (BMC) for excellent support.
This study was supported by the Peter Hans Hofschneider Professorship of the foundation
“Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent
within the framework of the German Excellence Initiative (to JR), and the Deutsche
Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to
JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from
the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled
and organized by Projekt DEAL.
article_number: e114557
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Arthur
full_name: Kuznetcov, Arthur
last_name: Kuznetcov
- first_name: Kasia
full_name: Stefanowski, Kasia
last_name: Stefanowski
- first_name: Monika D.
full_name: Hermann, Monika D.
last_name: Hermann
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Annette
full_name: Müller-Taubenberger, Annette
last_name: Müller-Taubenberger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557
apa: Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin,
J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid
migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557
chicago: Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika
D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg
Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.”
EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.
ieee: J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid
migration,” EMBO Journal. Embo Press, 2023.
ista: Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek
LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis
during amoeboid migration. EMBO Journal., e114557.
mla: Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid
Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.
short: J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin,
L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).
date_created: 2023-08-01T08:59:06Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2025-09-09T12:44:04Z
day: '21'
ddc:
- '570'
department:
- _id: NanoFab
- _id: Bio
doi: 10.15252/embj.2023114557
external_id:
isi:
- '001120971800001'
pmid:
- '37987147'
file:
- access_level: open_access
checksum: 6261d0041c7e8d284c39712c40079730
content_type: application/pdf
creator: dernst
date_created: 2023-11-27T08:45:56Z
date_updated: 2023-11-27T08:45:56Z
file_id: '14611'
file_name: 2023_EmboJournal_Kroll.pdf
file_size: 4862497
relation: main_file
success: 1
file_date_updated: 2023-11-27T08:45:56Z
fulldoi: https://doi.org/10.15252/embj.2023114557
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive pathfinding by nucleokinesis during amoeboid migration
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2023'
...
---
_id: '13447'
abstract:
- lang: eng
text: Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology
is a prime example, with oscillation periods and amplitudes that are readily detectable
with time-domain space-based telescopes. These oscillations can be used to infer
masses, ages and radii for large numbers of stars, providing unique constraints
on stellar populations in our galaxy. The cadence, duration, and spatial resolution
of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology
and will probe an important population not studied by prior missions. We identify
photometric precision as a key requirement for realizing the potential of asteroseismology
with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars
will enable detections of the populous red clump star population in the Galactic
bulge. If the survey efficiency is better than expected, we argue for repeat observations
of the same fields to improve photometric precision, or covering additional fields
to expand the stellar population reach if the photometric precision for saturated
stars is better than 1 mmag. Asteroseismology is relatively insensitive to the
timing of the observations during the mission, and the prime red clump targets
can be observed in a single 70 day campaign in any given field. Complementary
stellar characterization, particularly astrometry tied to the Gaia system, will
also dramatically expand the diagnostic power of asteroseismology. We also highlight
synergies to Roman GBTDS exoplanet science using transits and microlensing.
article_number: '2307.03237'
article_processing_charge: No
arxiv: 1
author:
- first_name: Daniel
full_name: Huber, Daniel
last_name: Huber
- first_name: Marc
full_name: Pinsonneault, Marc
last_name: Pinsonneault
- first_name: Paul
full_name: Beck, Paul
last_name: Beck
- first_name: Timothy R.
full_name: Bedding, Timothy R.
last_name: Bedding
- first_name: Joss Bland-Hawthorn
full_name: Joss Bland-Hawthorn, Joss Bland-Hawthorn
last_name: Joss Bland-Hawthorn
- first_name: Sylvain N.
full_name: Breton, Sylvain N.
last_name: Breton
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: William J.
full_name: Chaplin, William J.
last_name: Chaplin
- first_name: Rafael A.
full_name: Garcia, Rafael A.
last_name: Garcia
- first_name: Samuel K.
full_name: Grunblatt, Samuel K.
last_name: Grunblatt
- first_name: Joyce A.
full_name: Guzik, Joyce A.
last_name: Guzik
- first_name: Saskia
full_name: Hekker, Saskia
last_name: Hekker
- first_name: Steven D.
full_name: Kawaler, Steven D.
last_name: Kawaler
- first_name: Stephane
full_name: Mathis, Stephane
last_name: Mathis
- first_name: Savita
full_name: Mathur, Savita
last_name: Mathur
- first_name: Travis
full_name: Metcalfe, Travis
last_name: Metcalfe
- first_name: Benoit
full_name: Mosser, Benoit
last_name: Mosser
- first_name: Melissa K.
full_name: Ness, Melissa K.
last_name: Ness
- first_name: Anthony L.
full_name: Piro, Anthony L.
last_name: Piro
- first_name: Aldo
full_name: Serenelli, Aldo
last_name: Serenelli
- first_name: Sanjib
full_name: Sharma, Sanjib
last_name: Sharma
- first_name: David R.
full_name: Soderblom, David R.
last_name: Soderblom
- first_name: Keivan G.
full_name: Stassun, Keivan G.
last_name: Stassun
- first_name: Dennis
full_name: Stello, Dennis
last_name: Stello
- first_name: Jamie
full_name: Tayar, Jamie
last_name: Tayar
- first_name: Gerard T. van
full_name: Belle, Gerard T. van
last_name: Belle
- first_name: Joel C.
full_name: Zinn, Joel C.
last_name: Zinn
citation:
ama: Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic
bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237
apa: Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn,
J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman
galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237
chicago: Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn
Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology
with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.
ieee: D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain
survey,” arXiv. .
ista: Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton
SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler
SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma
S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology
with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.
mla: Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain
Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.
short: D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn,
S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik,
S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness,
A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J.
Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).
date_created: 2023-08-02T07:30:43Z
date_published: 2023-07-06T00:00:00Z
date_updated: 2023-08-02T07:36:00Z
day: '06'
department:
- _id: LiBu
doi: 10.48550/arXiv.2307.03237
external_id:
arxiv:
- '2307.03237'
fulldoi: https://doi.org/10.48550/arXiv.2307.03237
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2307.03237
month: '07'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Asteroseismology with the Roman galactic bulge time-domain survey
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13963'
abstract:
- lang: eng
text: The many-body localization (MBL) proximity effect is an intriguing phenomenon
where a thermal bath localizes due to the interaction with a disordered system.
The interplay of thermal and nonergodic behavior in these systems gives rise to
a rich phase diagram, whose exploration is an active field of research. In this
paper, we study a bosonic Hubbard model featuring two particle species representing
the bath and the disordered system. Using state-of-the-art numerical techniques,
we investigate the dynamics of the model in different regimes, based on which
we obtain a tentative phase diagram as a function of coupling strength and bath
size. When the bath is composed of a single particle, we observe clear signatures
of a transition from an MBL proximity effect to a delocalized phase. Increasing
the bath size, however, its thermalizing effect becomes stronger and eventually
the whole system delocalizes in the range of moderate interaction strengths studied.
In this regime, we characterize particle transport, revealing diffusive behavior
of the originally localized bosons.
acknowledgement: "We thank A. A. Michailidis and A. Mirlin for insightful discussions.
P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge
PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD
simulations were performed. The TEBD simulations were performed using the ITensor
library [60]."
article_number: '054201'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity
effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5).
doi:10.1103/physrevb.108.054201
apa: Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body
localization proximity effect in a two-species bosonic Hubbard model. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201
chicago: Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body
Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.
ieee: P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization
proximity effect in a two-species bosonic Hubbard model,” Physical Review B,
vol. 108, no. 5. American Physical Society, 2023.
ista: Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity
effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201.
mla: Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species
Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American
Physical Society, 2023, doi:10.1103/physrevb.108.054201.
short: P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).
corr_author: '1'
date_created: 2023-08-05T18:25:22Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2025-04-14T07:52:06Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevb.108.054201
ec_funded: 1
external_id:
arxiv:
- '2303.16876'
file:
- access_level: open_access
checksum: f763000339b5fd543c14377109920690
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T09:48:08Z
date_updated: 2023-08-07T09:48:08Z
file_id: '13981'
file_name: 2023_PhysRevB_Brighi.pdf
file_size: 3051398
relation: main_file
success: 1
file_date_updated: 2023-08-07T09:48:08Z
fulldoi: https://doi.org/10.1103/physrevb.108.054201
has_accepted_license: '1'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Many-body localization proximity effect in a two-species bosonic Hubbard model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13966'
abstract:
- lang: eng
text: We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation
energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams,
we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation
energies up to n=5, with quadratic scaling in the number of basis functions. Our
technique reduces the computational complexity of the molecular many-fermion correlation
problem, opening up the possibility of low-scaling, accurate stochastic computations
for a wide class of many-body systems described by Hugenholtz diagrams.
acknowledgement: We acknowledge stimulating discussions with Sergey Varganov, Artur
Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov,
Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from
the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L.
acknowledges support by the FWF under Project No. P29902-N27, and by the European
Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported
by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research
Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg
STRUCTURES Excellence Cluster). The authors acknowledge support by the state of
Baden-Württemberg through bwHPC.
article_number: '045115'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
orcid: 0000-0001-6889-1418
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: T. V.
full_name: Tscherbul, T. V.
last_name: Tscherbul
citation:
ama: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic
correlation in molecules: High-order many-body perturbation theory with low scaling.
Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115'
apa: 'Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic
Monte Carlo for electronic correlation in molecules: High-order many-body perturbation
theory with low scaling. Physical Review B. American Physical Society.
https://doi.org/10.1103/PhysRevB.108.045115'
chicago: 'Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic
Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation
Theory with Low Scaling.” Physical Review B. American Physical Society,
2023. https://doi.org/10.1103/PhysRevB.108.045115.'
ieee: 'G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte
Carlo for electronic correlation in molecules: High-order many-body perturbation
theory with low scaling,” Physical Review B, vol. 108, no. 4. American
Physical Society, 2023.'
ista: 'Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo
for electronic correlation in molecules: High-order many-body perturbation theory
with low scaling. Physical Review B. 108(4), 045115.'
mla: 'Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation
in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical
Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.'
short: G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).
corr_author: '1'
date_created: 2023-08-06T22:01:10Z
date_published: 2023-07-15T00:00:00Z
date_updated: 2025-09-09T12:45:32Z
day: '15'
department:
- _id: MiLe
- _id: TaHa
doi: 10.1103/PhysRevB.108.045115
ec_funded: 1
external_id:
arxiv:
- '2203.12666'
isi:
- '001532067800001'
fulldoi: https://doi.org/10.1103/PhysRevB.108.045115
intvolume: ' 108'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.12666
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Diagrammatic Monte Carlo for electronic correlation in molecules: High-order
many-body perturbation theory with low scaling'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 108
year: '2023'
...
---
_id: '13969'
abstract:
- lang: eng
text: "Bundling crossings is a strategy which can enhance the readability\r\nof
graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany
two edges have at most one common point which can be a common vertex or a\r\ncrossing.
Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation
of the bundled crossing number of a good drawing with no toothed\r\nhole. In general
the number of toothed holes has to be added to the 8-approximation.\r\nIn the
special case of circular drawings the approximation factor is 8, this improves\r\nupon
the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation
factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce.
We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe
pseudosegments is bipartite and has no toothed hole."
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1. An extended abstract of this paper has been published in
the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal
of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629
apa: Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled
crossing number. Journal of Graph Algorithms and Applications. Brown University.
https://doi.org/10.7155/jgaa.00629
chicago: Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” Journal of Graph Algorithms and Applications. Brown University,
2023. https://doi.org/10.7155/jgaa.00629.
ieee: A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,”
Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University,
pp. 433–457, 2023.
ista: Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number.
Journal of Graph Algorithms and Applications. 27(6), 433–457.
mla: Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6,
Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629.
short: A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications
27 (2023) 433–457.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-09-10T09:35:55Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.7155/jgaa.00629
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
file:
- access_level: open_access
checksum: 9c30d2b8e324cc1c904f2aeec92013a3
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T08:00:48Z
date_updated: 2023-08-07T08:00:48Z
file_id: '13979'
file_name: 2023_JourGraphAlgorithms_Arroyo.pdf
file_size: 865774
relation: main_file
success: 1
file_date_updated: 2023-08-07T08:00:48Z
fulldoi: https://doi.org/10.7155/jgaa.00629
has_accepted_license: '1'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 433-457
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Graph Algorithms and Applications
publication_identifier:
issn:
- 1526-1719
publication_status: published
publisher: Brown University
quality_controlled: '1'
related_material:
record:
- id: '11185'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Approximating the bundled crossing number
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2023'
...
---
_id: '13970'
article_processing_charge: No
article_type: original
author:
- first_name: Amiera
full_name: Madani, Amiera
last_name: Madani
- first_name: Eric T.
full_name: Sletten, Eric T.
last_name: Sletten
- first_name: Cristian
full_name: Cavedon, Cristian
last_name: Cavedon
- first_name: Peter H.
full_name: Seeberger, Peter H.
last_name: Seeberger
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
citation:
ama: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271
apa: Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B.
(2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271
chicago: Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger,
and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.
ieee: A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,”
Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.
ista: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 100, 271–286.
mla: Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.
short: A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses
100 (2023) 271–286.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-06-18T17:32:17Z
day: '01'
ddc:
- '540'
department:
- _id: BaPi
doi: 10.15227/orgsyn.100.0271
fulldoi: https://doi.org/10.15227/orgsyn.100.0271
intvolume: ' 100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15227/orgsyn.100.0271
month: '07'
oa: 1
oa_version: Published Version
page: 271-286
publication: Organic Syntheses
publication_identifier:
eissn:
- 2333-3553
issn:
- 0078-6209
publication_status: published
publisher: Organic Syntheses
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2023'
...
---
_id: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
fulldoi: https://doi.org/10.1038/s41567-023-02136-x
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional colloidal aggregation in chiral bacterial baths
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13972'
abstract:
- lang: eng
text: This Special Collection is dedicated to the field of photocatalytic synthesis
and contains a diverse selection of original research contributions. It includes
studies on catalyst development, mechanistic investigations, method development
and the use of enabling technologies, illustrating the many facets of state-of-the-art
research in photocatalytic synthesis. Further, emerging topics are surveyed and
discussed in three reviews and a concept article.
article_number: e202300683
article_processing_charge: No
article_type: letter_note
author:
- first_name: Line
full_name: Næsborg, Line
last_name: Næsborg
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Oliver S.
full_name: Wenger, Oliver S.
last_name: Wenger
citation:
ama: 'Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis.
ChemCatChem. 2023;15(17). doi:10.1002/cctc.202300683'
apa: 'Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic
synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683'
chicago: 'Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection:
Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.'
ieee: 'L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic
synthesis,” ChemCatChem, vol. 15, no. 17. Wiley, 2023.'
ista: 'Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic
synthesis. ChemCatChem. 15(17), e202300683.'
mla: 'Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem,
vol. 15, no. 17, e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.'
short: L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem 15 (2023).
corr_author: '1'
date_created: 2023-08-06T22:01:12Z
date_published: 2023-09-08T00:00:00Z
date_updated: 2026-06-18T17:32:51Z
day: '08'
ddc:
- '540'
department:
- _id: BaPi
doi: 10.1002/cctc.202300683
external_id:
isi:
- '001037859900001'
fulldoi: https://doi.org/10.1002/cctc.202300683
intvolume: ' 15'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/cctc.202300683
month: '09'
oa: 1
oa_version: Published Version
publication: ChemCatChem
publication_identifier:
eissn:
- 1867-3899
issn:
- 1867-3880
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Special Collection: Photocatalytic synthesis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '13976'
abstract:
- lang: eng
text: Conflicts and natural disasters affect entire populations of the countries
involved and, in addition to the thousands of lives destroyed, have a substantial
negative impact on the scientific advances these countries provide. The unprovoked
invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria,
and the ongoing conflicts in the Middle East are just a few examples. Millions
of people have been killed or displaced, their futures uncertain. These events
have resulted in extensive infrastructure collapse, with loss of electricity,
transportation, and access to services. Schools, universities, and research centers
have been destroyed along with decades’ worth of data, samples, and findings.
Scholars in disaster areas face short- and long-term problems in terms of what
they can accomplish now for obtaining grants and for employment in the long run.
In our interconnected world, conflicts and disasters are no longer a local problem
but have wide-ranging impacts on the entire world, both now and in the future.
Here, we focus on the current and ongoing impact of war on the scientific community
within Ukraine and from this draw lessons that can be applied to all affected
countries where scientists at risk are facing hardship. We present and classify
examples of effective and feasible mechanisms used to support researchers in countries
facing hardship and discuss how these can be implemented with help from the international
scientific community and what more is desperately needed. Reaching out, providing
accessible training opportunities, and developing collaborations should increase
inclusion and connectivity, support scientific advancements within affected communities,
and expedite postwar and disaster recovery.
acknowledgement: "Our article is dedicated to all freedom-loving people around the
world and to the people of Ukraine who fight for our freedom. Special thanks to
Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful
review, valuable criticism, and useful suggestions while preparing this manuscript,
and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered
their time. No funding supported work on this article."
article_number: giad045
article_processing_charge: Yes
article_type: review
author:
- first_name: Walter
full_name: Wolfsberger, Walter
last_name: Wolfsberger
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Khrystyna
full_name: Shchubelka, Khrystyna
last_name: Shchubelka
- first_name: Alina
full_name: Frolova, Alina
last_name: Frolova
- first_name: Yuriy
full_name: Salyha, Yuriy
last_name: Salyha
- first_name: Oksana
full_name: Zlenko, Oksana
last_name: Zlenko
- first_name: Mykhailo
full_name: Arych, Mykhailo
last_name: Arych
- first_name: Dmytro
full_name: Dziuba, Dmytro
last_name: Dziuba
- first_name: Andrii
full_name: Parkhomenko, Andrii
last_name: Parkhomenko
- first_name: Volodymyr
full_name: Smolanka, Volodymyr
last_name: Smolanka
- first_name: Zeynep H.
full_name: Gümüş, Zeynep H.
last_name: Gümüş
- first_name: Efe
full_name: Sezgin, Efe
last_name: Sezgin
- first_name: Alondra
full_name: Diaz-Lameiro, Alondra
last_name: Diaz-Lameiro
- first_name: Viktor R.
full_name: Toth, Viktor R.
last_name: Toth
- first_name: Megi
full_name: Maci, Megi
last_name: Maci
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Patricia M.
full_name: Morton, Patricia M.
last_name: Morton
- first_name: Paweł P.
full_name: Łabaj, Paweł P.
last_name: Łabaj
- first_name: Veronika
full_name: Romero, Veronika
last_name: Romero
- first_name: Jakub
full_name: Hlávka, Jakub
last_name: Hlávka
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
- first_name: Taras K.
full_name: Oleksyk, Taras K.
last_name: Oleksyk
citation:
ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders:
Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045'
apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko,
O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine.
GigaScience. Oxford University Press. https://doi.org/10.1093/gigascience/giad045'
chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova,
Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders:
Lessons from Ukraine.” GigaScience. Oxford University Press, 2023. https://doi.org/10.1093/gigascience/giad045.'
ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,”
GigaScience, vol. 12. Oxford University Press, 2023.'
ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych
M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth
VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul
S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience.
12, giad045.'
mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.”
GigaScience, vol. 12, giad045, Oxford University Press, 2023, doi:10.1093/gigascience/giad045.'
short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko,
M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro,
V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero,
J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).
date_created: 2023-08-06T22:01:13Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2026-06-18T17:33:34Z
day: '27'
ddc:
- '000'
department:
- _id: FyKo
doi: 10.1093/gigascience/giad045
external_id:
isi:
- '001081086100001'
pmid:
- '37496156'
fulldoi: https://doi.org/10.1093/gigascience/giad045
intvolume: ' 12'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/gigascience/giad045
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: GigaScience
publication_identifier:
eissn:
- 2047-217X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/gigascience/giad066
scopus_import: '1'
status: public
title: 'Scientists without borders: Lessons from Ukraine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '14037'
abstract:
- lang: eng
text: 'Traditionally, nuclear spin is not considered to affect biological processes.
Recently, this has changed as isotopic fractionation that deviates from classical
mass dependence was reported both in vitro and in vivo. In these cases, the isotopic
effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects
using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial
dioxygen production system and biological aquaporin channels in cells. We observe
that oxygen dynamics in chiral environments (in particular its transport) depend
on nuclear spin, suggesting future applications for controlled isotope separation
to be used, for instance, in NMR. To demonstrate the mechanism behind our findings,
we formulate theoretical models based on a nuclear-spin-enhanced switch between
electronic spin states. Accounting for the role of nuclear spin in biology can
provide insights into the role of quantum effects in living systems and help inspire
the development of future biotechnology solutions.'
acknowledgement: N.M.-S. acknowledges the support of the Ministry of Energy, Israel,
as part of the scholarship program for graduate students in the fields of energy.
M.L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation,
Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support
of the BSF-NSF 094 Grant No. 2022503.
article_number: e2300828120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ofek
full_name: Vardi, Ofek
last_name: Vardi
- first_name: Naama
full_name: Maroudas-Sklare, Naama
last_name: Maroudas-Sklare
- first_name: Yuval
full_name: Kolodny, Yuval
last_name: Kolodny
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Amijai
full_name: Saragovi, Amijai
last_name: Saragovi
- first_name: Nir
full_name: Galili, Nir
last_name: Galili
- first_name: Stav
full_name: Ferrera, Stav
last_name: Ferrera
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Nir
full_name: Yuran, Nir
last_name: Yuran
- first_name: Hagit P.
full_name: Affek, Hagit P.
last_name: Affek
- first_name: Boaz
full_name: Luz, Boaz
last_name: Luz
- first_name: Yonaton
full_name: Goldsmith, Yonaton
last_name: Goldsmith
- first_name: Nir
full_name: Keren, Nir
last_name: Keren
- first_name: Shira
full_name: Yochelis, Shira
last_name: Yochelis
- first_name: Itay
full_name: Halevy, Itay
last_name: Halevy
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
citation:
ama: Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological
processes. Proceedings of the National Academy of Sciences of the United States
of America. 2023;120(32). doi:10.1073/pnas.2300828120
apa: Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili,
N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2300828120
chicago: Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai
Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological
Processes.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.
ieee: O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32. National Academy of Sciences, 2023.
ista: Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N,
Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis
S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes.
Proceedings of the National Academy of Sciences of the United States of America.
120(32), e2300828120.
mla: Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.
short: O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili,
S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren,
S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy
of Sciences of the United States of America 120 (2023).
date_created: 2023-08-13T22:01:12Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2025-09-09T12:47:53Z
day: '31'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2300828120
ec_funded: 1
external_id:
isi:
- '001121663600001'
pmid:
- '37523549'
file:
- access_level: open_access
checksum: a5ed64788a5acef9b9a300a26fa5a177
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:43:45Z
date_updated: 2023-08-14T07:43:45Z
file_id: '14047'
file_name: 2023_PNAS_Vardi.pdf
file_size: 1003092
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:43:45Z
fulldoi: https://doi.org/10.1073/pnas.2300828120
has_accepted_license: '1'
intvolume: ' 120'
isi: 1
issue: '32'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear spin effects in biological processes
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 120
year: '2023'
...
---
_id: '14039'
abstract:
- lang: eng
text: Membranes are essential for life. They act as semi-permeable boundaries that
define cells and organelles. In addition, their surfaces actively participate
in biochemical reaction networks, where they confine proteins, align reaction
partners, and directly control enzymatic activities. Membrane-localized reactions
shape cellular membranes, define the identity of organelles, compartmentalize
biochemical processes, and can even be the source of signaling gradients that
originate at the plasma membrane and reach into the cytoplasm and nucleus. The
membrane surface is, therefore, an essential platform upon which myriad cellular
processes are scaffolded. In this review, we summarize our current understanding
of the biophysics and biochemistry of membrane-localized reactions with particular
focus on insights derived from reconstituted and cellular systems. We discuss
how the interplay of cellular factors results in their self-organization, condensation,
assembly, and activity, and the emergent properties derived from them.
acknowledgement: We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B,
and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program (grant agreement no. 101045340 to M.L.). We are grateful
for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic,
Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas A.
full_name: Leonard, Thomas A.
last_name: Leonard
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Sascha
full_name: Martens, Sascha
last_name: Martens
citation:
ama: Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes
cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332.
doi:10.1016/j.devcel.2023.06.001
apa: Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as
a platform that organizes cellular and biochemical processes. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001
chicago: Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface
as a Platform That Organizes Cellular and Biochemical Processes.” Developmental
Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001.
ieee: T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform
that organizes cellular and biochemical processes,” Developmental Cell,
vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.
ista: Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that
organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332.
mla: Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes
Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15,
Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001.
short: T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.
corr_author: '1'
date_created: 2023-08-13T22:01:12Z
date_published: 2023-08-07T00:00:00Z
date_updated: 2024-10-22T11:40:18Z
day: '07'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.devcel.2023.06.001
external_id:
isi:
- '001059110400001'
pmid:
- '37419118'
file:
- access_level: open_access
checksum: d8c5dc97cd40c26da2ec98ae723ab368
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:57:55Z
date_updated: 2023-08-14T07:57:55Z
file_id: '14049'
file_name: 2023_DevelopmentalCell_Leonard.pdf
file_size: 3184217
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:57:55Z
fulldoi: https://doi.org/10.1016/j.devcel.2023.06.001
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1315-1332
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
- _id: bd6ae2ca-d553-11ed-ba76-a4aa239da5ee
grant_number: '101045340'
name: Synthetic and structural biology of Rab GTPase networks
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The membrane surface as a platform that organizes cellular and biochemical
processes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2023'
...
---
_id: '14040'
abstract:
- lang: eng
text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure
efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex.
The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction
center polypeptide and promotes the initial steps of PSII assembly, but its binding
site is unclear. Here we use cryo-electron microscopy to determine the structure
of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached.
Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that
ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the
premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions
with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall,
our work provides valuable insights into the early stages of PSII assembly and
the structural changes that create the binding site for the Mn4CaO5 cluster.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology
& Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J.
Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project
19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the
IST high-performance computing cluster.
article_number: '4681'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
last_name: Zhao
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Jana
full_name: Knoppová, Jana
last_name: Knoppová
- first_name: Roman
full_name: Sobotka, Roman
last_name: Sobotka
- first_name: James W.
full_name: Murray, James W.
last_name: Murray
- first_name: Peter J.
full_name: Nixon, Peter J.
last_name: Nixon
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Josef
full_name: Komenda, Josef
last_name: Komenda
citation:
ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies
the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6
apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon,
P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6
chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray,
Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor
Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem
II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.
ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov
LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving
manganese cluster during photosystem II biogenesis. Nature Communications. 14,
4681.
mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving
Manganese Cluster during Photosystem II Biogenesis.” Nature Communications,
vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.
short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon,
L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2025-04-23T13:05:33Z
day: '04'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-023-40388-6
external_id:
isi:
- '001042606700004'
pmid:
- '37542031'
file:
- access_level: open_access
checksum: 3b9043df3d51c300f9be95eac3ff9d0b
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:01:12Z
date_updated: 2023-08-14T07:01:12Z
file_id: '14044'
file_name: 2023_NatureComm_Zhao.pdf
file_size: 2315325
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:01:12Z
fulldoi: https://doi.org/10.1038/s41467-023-40388-6
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese
cluster during photosystem II biogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14041'
abstract:
- lang: eng
text: Tissue morphogenesis and patterning during development involve the segregation
of cell types. Segregation is driven by differential tissue surface tensions generated
by cell types through controlling cell-cell contact formation by regulating adhesion
and actomyosin contractility-based cellular cortical tensions. We use vertebrate
tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional
heterotypic segregation and developed a quantitative analysis of their dynamics
based on 3D time-lapse microscopy. We show that general inhibition of actomyosin
contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific
inhibition of non-muscle myosin2 activity by overexpression of myosin assembly
inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction
during aggregation and inverted geometry observed during segregation. The same
is observed when we express a constitutively active Rho kinase isoform to ubiquitously
keep actomyosin contractility high at cell-cell and cell-medium interfaces and
thus overriding the interface-specific regulation of cortical tensions. Tissue
surface tension regulation can become an effective tool in tissue engineering.
acknowledgement: "We thank Marton Gulyas (ELTE Eötvös University) for development
of videomicroscopy experiment manager and image analysis software. Authors are grateful
to Gabor Forgacs (University of Missouri) for critical reading of earlier versions
of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University)
for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project
No 227878 to TV, the National Research Development and Innovation Fund of Hungary,
K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by
the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access
funding provided by Eötvös Loránd University."
article_number: '817'
article_processing_charge: Yes
article_type: original
author:
- first_name: Elod
full_name: Méhes, Elod
last_name: Méhes
- first_name: Enys
full_name: Mones, Enys
last_name: Mones
- first_name: Máté
full_name: Varga, Máté
last_name: Varga
- first_name: Áron
full_name: Zsigmond, Áron
last_name: Zsigmond
- first_name: Beáta
full_name: Biri-Kovács, Beáta
last_name: Biri-Kovács
- first_name: László
full_name: Nyitray, László
last_name: Nyitray
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Tamás
full_name: Vicsek, Tamás
last_name: Vicsek
citation:
ama: Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology.
2023;6. doi:10.1038/s42003-023-05181-7
apa: Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L.,
… Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by
tissue surface tension regulation. Communications Biology. Springer Nature.
https://doi.org/10.1038/s42003-023-05181-7
chicago: Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács,
László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and
Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue
Surface Tension Regulation.” Communications Biology. Springer Nature, 2023.
https://doi.org/10.1038/s42003-023-05181-7.
ieee: E. Méhes et al., “3D cell segregation geometry and dynamics are governed
by tissue surface tension regulation,” Communications Biology, vol. 6.
Springer Nature, 2023.
ista: Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V,
Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology. 6,
817.
mla: Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed
by Tissue Surface Tension Regulation.” Communications Biology, vol. 6,
817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.
short: E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V.
Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2023-12-13T12:07:33Z
day: '04'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1038/s42003-023-05181-7
external_id:
isi:
- '001042544100001'
pmid:
- '37542157'
file:
- access_level: open_access
checksum: 1f9324f736bdbb76426b07736651c4cd
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:17:36Z
date_updated: 2023-08-14T07:17:36Z
file_id: '14045'
file_name: 2023_CommBiology_Mehes.pdf
file_size: 10181997
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:17:36Z
fulldoi: https://doi.org/10.1038/s42003-023-05181-7
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3D cell segregation geometry and dynamics are governed by tissue surface tension
regulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2023'
...
---
_id: '14043'
abstract:
- lang: eng
text: 'Over the last two decades, a significant line of work in theoretical algorithms
has made progress in solving linear systems of the form Lx=b, where L is the Laplacian
matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x
of the linear system can be interpreted as the potentials of an electrical flow
in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings
of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013.
https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time
algorithm that maintains the Kirchoff Current Law, and gradually enforces the
Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this
paper, we consider a dual version of the algorithm that maintains the Kirchoff
Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling:
each iteration updates all potentials on one side of a fundamental cut of a spanning
tree by the same amount. We prove that this dual algorithm also runs in a near-linear
number of iterations. We show, however, that if we abstract cut toggling as a
natural data structure problem, this problem can be reduced to the online vector–matrix-vector
problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger
et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing,
pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies
that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and
thus a straightforward implementation of the cut-toggling algorithm requires essentially
linear time per iteration. To circumvent the lower bound, we batch update steps,
and perform them simultaneously instead of sequentially. An appropriate choice
of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian
systems. Furthermore, we show that if we sparsify the graph and call our algorithm
recursively on the Laplacian system implied by batching and sparsifying, we can
reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm
can achieve (almost) the same running time as its primal cycle-toggling counterpart.'
acknowledgement: Monika Henzinger was supported by funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms
for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from
the netidee SCIENCE Stiftung, 2020–2024. Billy Jin was Supported in part by NSERC
fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported
in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson
was supported in part by NSF grant CCF-2007009.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Billy
full_name: Jin, Billy
last_name: Jin
- first_name: Richard
full_name: Peng, Richard
last_name: Peng
- first_name: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: Henzinger M, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm
for solving Laplacian linear systems. Algorithmica. 2023;85:2680-3716.
doi:10.1007/s00453-023-01154-8
apa: Henzinger, M., Jin, B., Peng, R., & Williamson, D. P. (2023). A combinatorial
cut-toggling algorithm for solving Laplacian linear systems. Algorithmica.
Springer Nature. https://doi.org/10.1007/s00453-023-01154-8
chicago: Henzinger, Monika, Billy Jin, Richard Peng, and David P. Williamson. “A
Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” Algorithmica.
Springer Nature, 2023. https://doi.org/10.1007/s00453-023-01154-8.
ieee: M. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling
algorithm for solving Laplacian linear systems,” Algorithmica, vol. 85.
Springer Nature, pp. 2680–3716, 2023.
ista: Henzinger M, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling
algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.
mla: Henzinger, Monika, et al. “A Combinatorial Cut-Toggling Algorithm for Solving
Laplacian Linear Systems.” Algorithmica, vol. 85, Springer Nature, 2023,
pp. 2680–3716, doi:10.1007/s00453-023-01154-8.
short: M. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716.
date_created: 2023-08-13T22:01:13Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2025-04-15T06:24:05Z
day: '01'
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- _id: MoHe
doi: 10.1007/s00453-023-01154-8
ec_funded: 1
external_id:
arxiv:
- '2010.16316'
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month: '12'
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page: 2680-3716
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call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
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name: Fast Algorithms for a Reactive Network Layer
publication: Algorithmica
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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title: A combinatorial cut-toggling algorithm for solving Laplacian linear systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2023'
...
---
OA_place: publisher
_id: '14058'
abstract:
- lang: eng
text: "Females and males across species are subject to divergent selective pressures
arising\r\nfrom di↵erent reproductive interests and ecological niches. This often
translates into a\r\nintricate array of sex-specific natural and sexual selection
on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic
sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution
of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual
dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications
of the genetic networks ultimately linked to sex-determining\r\ntranscription
factors. Although much empirical and theoretical evidence supports this\r\nstandard
picture of the molecular basis of sexual conflict resolution, there still are
a\r\nfew open questions regarding the complex array of selective forces driving
phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms
underlying sexspecific adaptation. I address some of these open questions in my
PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within
populations,\r\nas a response to the temporal and spatial changes in sex-specific
selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific
phenotypic variation along\r\nthree life stages and across populations spanning
the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm,
in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns
lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying
the observed transcriptomic variation? I\r\naddress this question by examining
the sex- and tissue-specific expression variation in\r\nnewly-generated datasets
of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster.
I additionally used two complementary approaches for the study of the\r\ngenetic
basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe
thesis.\r\nThird, how does intersex correlation, thought to be one of the main
aspects constraining the ability for the two sexes to decouple, interact with
the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing
selection, mutation and drift\r\nto formalize common intuition regarding the patterns
of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth
Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides
useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic
layers of sex-specific variation,\r\nand contributes to our general understanding
of the dynamics of sexual dimorphism\r\nevolution."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058'
apa: 'Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058'
chicago: 'Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14058.'
ieee: 'G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria.'
mla: 'Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14058.'
short: 'G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and
Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.'
corr_author: '1'
date_created: 2023-08-15T10:20:40Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2026-04-07T13:25:34Z
day: '15'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/at:ista:14058
ec_funded: 1
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: '230'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication_identifier:
isbn:
- 978-3-99078-035-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9803'
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status: public
- id: '12933'
relation: research_data
status: public
- id: '6831'
relation: part_of_dissertation
status: public
- id: '14077'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization
of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation'
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '14076'
abstract:
- lang: eng
text: Hyperproperties are properties that relate multiple execution traces. Previous
work on monitoring hyperproperties focused on synchronous hyperproperties, usually
specified in HyperLTL. When monitoring synchronous hyperproperties, all traces
are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers
and show how to use them for monitoring synchronous as well as, for the first
time, asynchronous hyperproperties. Prefix transducers map multiple input traces
into one or more output traces by incrementally matching prefixes of the input
traces against expressions similar to regular expressions. The prefixes of different
traces which are consumed by a single matching step of the monitor may have different
lengths. The deterministic and executable nature of prefix transducers makes them
more suitable as an intermediate formalism for runtime verification than logical
specifications, which tend to be highly non-deterministic, especially in the case
of asynchronous hyperproperties. We report on a set of experiments about monitoring
asynchronous version of observational determinism.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank Ana Oliveira da Costa for commenting on a draft of the
paper.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers.
In: 23nd International Conference on Runtime Verification. Vol 14245. Springer
Nature; 2023:168-190. doi:10.1007/978-3-031-44267-4_9'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with
prefix transducers. In 23nd International Conference on Runtime Verification
(Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_9'
chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with
Prefix Transducers.” In 23nd International Conference on Runtime Verification,
14245:168–90. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_9.
ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,”
in 23nd International Conference on Runtime Verification, Thessaloniki,
Greek, 2023, vol. 14245, pp. 168–190.
ista: 'Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers.
23nd International Conference on Runtime Verification. RV: Conference on Runtime
Verification, LNCS, vol. 14245, 168–190.'
mla: Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix
Transducers.” 23nd International Conference on Runtime Verification, vol.
14245, Springer Nature, 2023, pp. 168–90, doi:10.1007/978-3-031-44267-4_9.
short: M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime
Verification, Springer Nature, 2023, pp. 168–190.
conference:
end_date: 2023-10-07
location: Thessaloniki, Greek
name: 'RV: Conference on Runtime Verification'
start_date: 2023-10-04
corr_author: '1'
date_created: 2023-08-16T20:46:08Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:42:55Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-44267-4_9
ec_funded: 1
file:
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checksum: ee33bd6f1a26f4dae7a8192584869fd8
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creator: dernst
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date_updated: 2023-10-16T07:15:11Z
file_id: '14430'
file_name: 2023_LNCS_RV_Chalupa.pdf
file_size: 867256
relation: main_file
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file_date_updated: 2023-10-16T07:15:11Z
fulldoi: https://doi.org/10.1007/978-3-031-44267-4_9
has_accepted_license: '1'
intvolume: ' 14245'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 168-190
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 23nd International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-031-44267-4
isbn:
- 978-3-031-44266-7
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Monitoring hyperproperties with prefix transducers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14245
year: '2023'
...