---
OA_place: publisher
OA_type: hybrid
_id: '20807'
abstract:
- lang: eng
text: Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group
is an important target for therapy in neurological disorders and an established
tumor marker. However, its physiological functions remain unclear. To better understand
general roles, we used the model organism Caenorhabditis elegans to genetically
manipulate its three existing orthologous genes and evaluate the impact on worm
physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs
affect the pharyngeal physiology, reproduction, and structural integrity of the
organism. Promoter-driven GFP expression revealed distinct localization for each
of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine,
and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3
located in the excretory cell. The present study provides new insight into the
unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific
tissue localizations. We believe that elucidation of particular roles in a non-mammalian
organism can help to explain important questions linked to physiology of this
protease group and in extension to human GCP2 involvement in pathophysiological
processes.
article_number: BSR20230502
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lucie
full_name: Panska, Lucie
last_name: Panska
- first_name: Stepanka
full_name: Nedvedova, Stepanka
last_name: Nedvedova
- first_name: Vojtech
full_name: Vacek, Vojtech
last_name: Vacek
- first_name: Daniela
full_name: Krivska, Daniela
last_name: Krivska
- first_name: Lukas
full_name: Konecny, Lukas
last_name: Konecny
- first_name: Filip
full_name: Knop, Filip
id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69
last_name: Knop
orcid: 0000-0002-3845-3465
- first_name: Zsofia
full_name: Kutil, Zsofia
last_name: Kutil
- first_name: Lubica
full_name: Skultetyova, Lubica
last_name: Skultetyova
- first_name: Adrian
full_name: Leontovyc, Adrian
last_name: Leontovyc
- first_name: Lenka
full_name: Ulrychova, Lenka
last_name: Ulrychova
- first_name: Judy
full_name: Sakanari, Judy
last_name: Sakanari
- first_name: Masako
full_name: Asahina, Masako
last_name: Asahina
- first_name: Cyril
full_name: Barinka, Cyril
last_name: Barinka
- first_name: Marie
full_name: Macurkova, Marie
last_name: Macurkova
- first_name: Jan
full_name: Dvorak, Jan
last_name: Dvorak
citation:
ama: Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate
carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports.
2024;44(1). doi:10.1042/bsr20230502
apa: Panska, L., Nedvedova, S., Vacek, V., Krivska, D., Konecny, L., Knop, F., …
Dvorak, J. (2024). Uncovering the essential roles of glutamate carboxypeptidase
2 orthologs in Caenorhabditis elegans. Bioscience Reports. Portland Press.
https://doi.org/10.1042/bsr20230502
chicago: Panska, Lucie, Stepanka Nedvedova, Vojtech Vacek, Daniela Krivska, Lukas
Konecny, Filip Knop, Zsofia Kutil, et al. “Uncovering the Essential Roles of Glutamate
Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports.
Portland Press, 2024. https://doi.org/10.1042/bsr20230502.
ieee: L. Panska et al., “Uncovering the essential roles of glutamate carboxypeptidase
2 orthologs in Caenorhabditis elegans,” Bioscience Reports, vol. 44, no.
1. Portland Press, 2024.
ista: Panska L, Nedvedova S, Vacek V, Krivska D, Konecny L, Knop F, Kutil Z, Skultetyova
L, Leontovyc A, Ulrychova L, Sakanari J, Asahina M, Barinka C, Macurkova M, Dvorak
J. 2024. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs
in Caenorhabditis elegans. Bioscience Reports. 44(1), BSR20230502.
mla: Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase
2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports, vol. 44, no.
1, BSR20230502, Portland Press, 2024, doi:10.1042/bsr20230502.
short: L. Panska, S. Nedvedova, V. Vacek, D. Krivska, L. Konecny, F. Knop, Z. Kutil,
L. Skultetyova, A. Leontovyc, L. Ulrychova, J. Sakanari, M. Asahina, C. Barinka,
M. Macurkova, J. Dvorak, Bioscience Reports 44 (2024).
date_created: 2025-12-12T09:03:54Z
date_published: 2024-01-12T00:00:00Z
date_updated: 2025-12-15T10:21:56Z
day: '12'
ddc:
- '570'
doi: 10.1042/bsr20230502
extern: '1'
external_id:
pmid:
- '38108122 '
has_accepted_license: '1'
intvolume: ' 44'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BSR20230502
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bioscience Reports
publication_identifier:
eissn:
- 1573-4935
issn:
- 0144-8463
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in
Caenorhabditis elegans
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: 44
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20808'
abstract:
- lang: eng
text: During Caenorhabditis elegans development, multiple cells migrate long distances
or extend processes to reach their final position and/or attain proper shape.
The Wnt signalling pathway stands out as one of the major coordinators of cell
migration or cell outgrowth along the anterior-posterior body axis. The outcome
of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In
this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated
kinase AAK1, acts together with the retromer complex as a positive regulator of
EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At
the same time, SEL-5 in cooperation with the retromer complex is also required
during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not
required for its role in neuronal migration or excretory cell outgrowth, and neither
of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish
that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2,
positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled
together generate a stop signal inhibiting its extension.
article_number: e91054
article_processing_charge: Yes
article_type: original
author:
- first_name: Filip
full_name: Knop, Filip
id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69
last_name: Knop
orcid: 0000-0002-3845-3465
- first_name: Apolena
full_name: Zounarová, Apolena
last_name: Zounarová
- first_name: Vojtěch
full_name: Šabata, Vojtěch
last_name: Šabata
- first_name: Teije Corneel
full_name: Middelkoop, Teije Corneel
last_name: Middelkoop
- first_name: Marie
full_name: Macůrková, Marie
last_name: Macůrková
citation:
ama: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. Caenorhabditis elegans
SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase
activity. eLife. 2024;13. doi:10.7554/elife.91054
apa: Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., & Macůrková, M.
(2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth
independently of its kinase activity. ELife. eLife Sciences Publications.
https://doi.org/10.7554/elife.91054
chicago: Knop, Filip, Apolena Zounarová, Vojtěch Šabata, Teije Corneel Middelkoop,
and Marie Macůrková. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration
and Cell Outgrowth Independently of Its Kinase Activity.” ELife. eLife
Sciences Publications, 2024. https://doi.org/10.7554/elife.91054.
ieee: F. Knop, A. Zounarová, V. Šabata, T. C. Middelkoop, and M. Macůrková, “Caenorhabditis
elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of
its kinase activity,” eLife, vol. 13. eLife Sciences Publications, 2024.
ista: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. 2024. Caenorhabditis
elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of
its kinase activity. eLife. 13, e91054.
mla: Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration
and Cell Outgrowth Independently of Its Kinase Activity.” ELife, vol. 13,
e91054, eLife Sciences Publications, 2024, doi:10.7554/elife.91054.
short: F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13
(2024).
date_created: 2025-12-12T09:06:31Z
date_published: 2024-07-19T00:00:00Z
date_updated: 2025-12-15T10:26:56Z
day: '19'
doi: 10.7554/elife.91054
extern: '1'
external_id:
pmid:
- '39028260'
intvolume: ' 13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/elife.91054
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: Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth
independently of its kinase activity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9651'
abstract:
- lang: eng
text: We introduce a hierachy of equivalence relations on the set of separated nets
of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞).
Two separated nets are called ϕ-displacement equivalent if, roughly speaking,
there is a bijection between them which, for large radii R, displaces points of
norm at most R by something of order at most ϕ(R). We show that the spectrum of
ϕ-displacement equivalence spans from the established notion of bounded displacement
equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation,
coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between
the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown
to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞.
We further undertake a comparison of our notion of ϕ-displacement equivalence
with previously studied relations on separated nets. Particular attention is given
to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz
equivalence.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). This work was started while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.
It was continued when the first named author was employed at University of Leipzig
and the second named author was employed at Institute of Science and Technology
of Austria, where he was supported by an IST Fellowship.'
article_number: '15'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Divergence of separated nets with respect to displacement
equivalence. Geometriae Dedicata. 2024;218. doi:10.1007/s10711-023-00862-3
apa: Dymond, M., & Kaluza, V. (2024). Divergence of separated nets with respect
to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3
chicago: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with
Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature,
2024. https://doi.org/10.1007/s10711-023-00862-3.
ieee: M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement
equivalence,” Geometriae Dedicata, vol. 218. Springer Nature, 2024.
ista: Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement
equivalence. Geometriae Dedicata. 218, 15.
mla: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect
to Displacement Equivalence.” Geometriae Dedicata, vol. 218, 15, Springer
Nature, 2024, doi:10.1007/s10711-023-00862-3.
short: M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024).
corr_author: '1'
date_created: 2021-07-14T07:01:27Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-04-23T07:37:26Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/s10711-023-00862-3
external_id:
arxiv:
- '2102.13046'
isi:
- '001105681500001'
pmid:
- '38021107'
file:
- access_level: open_access
checksum: 9418534ac2f3d6f1f091a8b8ccaed01e
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creator: dernst
date_created: 2024-07-16T10:14:13Z
date_updated: 2024-07-16T10:14:13Z
file_id: '17257'
file_name: 2024_GeometriaeDedicata_Dymond.pdf
file_size: 540981
relation: main_file
success: 1
file_date_updated: 2024-07-16T10:14:13Z
has_accepted_license: '1'
intvolume: ' 218'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Geometriae Dedicata
publication_identifier:
eissn:
- 1572-9168
issn:
- 0046-5755
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence of separated nets with respect to displacement equivalence
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: 218
year: '2024'
...
---
APC_amount: 6828 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17202'
abstract:
- lang: eng
text: Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions
have recently emerged as building blocks for hybrid quantum circuits. In this
study, we present a gatemon fabricated in planar Germanium. We induce superconductivity
in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which
separates the superconductor from the Ge quantum well. The Josephson junction
is then integrated into an Xmon circuit and capacitively coupled to a transmission
line resonator. We showcase the qubit tunability in a broad frequency range with
resonator and two-tone spectroscopy. Time-domain characterizations reveal energy
relaxation and coherence times up to 75 ns. Our results, combined with the recent
advances in the spin qubit field, pave the way towards novel hybrid and protected
qubits in a group IV, CMOS-compatible material.
acknowledged_ssus:
- _id: ScienComp
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten
Kjaergard and Javad Shabani for their valuable insights and comments. This research
was supported by the Scientific Service Units of ISTA through resources provided
by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and
related results were made possible with the support of the NOMIS Foundation and
the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge
the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial
support."
article_number: '6400'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Alessandro
full_name: Crippa, Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Levon
full_name: Baghumyan, Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- first_name: Giorgio
full_name: Fabris, Giorgio
id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352
last_name: Fabris
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar
Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6
apa: Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G.,
… Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-50763-6
chicago: Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan,
Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar
Ge.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6.
ieee: O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature
Communications, vol. 15. Springer Nature, 2024.
ista: Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani
F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable
transmon qubit in planar Ge. Nature Communications. 15, 6400.
mla: Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature
Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6.
short: O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor,
F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature
Communications 15 (2024).
corr_author: '1'
date_created: 2024-07-04T11:40:45Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-04-07T13:01:55Z
day: '30'
ddc:
- '530'
department:
- _id: GeKa
- _id: JoFi
- _id: GradSch
doi: 10.1038/s41467-024-50763-6
external_id:
arxiv:
- '2403.16774'
isi:
- '001281271000022'
pmid:
- '39080279'
file:
- access_level: open_access
checksum: ddf5361dcb6c543e2cea818501c09910
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:38:01Z
date_updated: 2024-08-05T08:38:01Z
file_id: '17388'
file_name: 2024_NatureComm_Sagi.pdf
file_size: 1928001
relation: main_file
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file_date_updated: 2024-08-05T08:38:01Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-024-53910-1
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A gate tunable transmon qubit in planar Ge
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
_id: '17203'
abstract:
- lang: eng
text: "The behavior of a rigid body primarily depends on its mass moments, which
consist of the mass, center of mass, and moments of inertia. It is possible to
manipulate these quantities without altering the geometric appearance of an object
by introducing cavities in its interior. Algorithms that find cavities of suitable
shapes and sizes have enabled the computational design of spinning tops, yo-yos,
wheels, buoys, and statically balanced objects. Previous work is based, for example,
on topology optimization on voxel grids, which introduces a large number of optimization
variables and box constraints, or offset surface computation, which cannot guarantee
that solutions to a feasible problem will always be found.\r\n\r\nIn this work,
we provide a mathematical analysis of constrained topology optimization problems
that depend only on mass moments. This class of problems covers, among others,
all applications mentioned above. Our main result is to show that no matter the
outer shape of the rigid body to be optimized or the optimization objective and
constraints considered, the optimal solution always features a quadric-shaped
interface between material and cavities. This proves that optimal interfaces are
always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases,
such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization
problem with a provably equivalent non-linear equation system in a small number
(<10) of variables, which represent the coefficients of the quadric. This system
can be solved in a few seconds for most examples, provides insights into the geometric
structure of many specific applications, and lets us describe their solution properties.
Finally, our method integrates seamlessly into modern fabrication workflows because
our solutions are analytical surfaces that are native to the CAD domain."
acknowledgement: We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans
code for this project, Stefan Jeschke for his help with the photographs, Malina
Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous
reviewers as well as the members of the ISTA Visual Computing Group for their feedback.
This project was funded in part by the European Research Council (ERC Consolidator
Grant 101045083 CoDiNA).
article_number: '78'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Mickaël
full_name: Ly, Mickaël
id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1
last_name: Ly
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization
problems that depend only on mass moments. Transactions on Graphics. 2024;43(4).
doi:10.1145/3658194'
apa: 'Hafner, C., Ly, M., & Wojtan, C. (2024). Spin-it faster: Quadrics solve
all topology optimization problems that depend only on mass moments. Transactions
on Graphics. Denver, Colorado: Association for Computing Machinery. https://doi.org/10.1145/3658194'
chicago: 'Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics
Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions
on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658194.'
ieee: 'C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology
optimization problems that depend only on mass moments,” Transactions on Graphics,
vol. 43, no. 4. Association for Computing Machinery, 2024.'
ista: 'Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology
optimization problems that depend only on mass moments. Transactions on Graphics.
43(4), 78.'
mla: 'Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization
Problems That Depend Only on Mass Moments.” Transactions on Graphics, vol.
43, no. 4, 78, Association for Computing Machinery, 2024, doi:10.1145/3658194.'
short: C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).
conference:
end_date: 2024-08-01
location: Denver, Colorado
start_date: 2024-07-28
corr_author: '1'
date_created: 2024-07-05T12:08:57Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:29:09Z
day: '01'
ddc:
- '516'
department:
- _id: ChWo
doi: 10.1145/3658194
external_id:
isi:
- '001289270900045'
file:
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content_type: application/pdf
creator: chafner
date_created: 2024-07-05T12:05:17Z
date_updated: 2024-07-05T12:05:17Z
file_id: '17204'
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file_size: 7225150
relation: main_file
success: 1
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content_type: application/pdf
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file_id: '17205'
file_name: sif-supp-final.pdf
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file_id: '17276'
file_name: sif-video-final.mp4
file_size: 170001305
relation: supplementary_material
title: Submission Video
file_date_updated: 2024-07-17T09:29:13Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '4'
keyword:
- Topology Optimization
- Mass Moments
- Computational Geometry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spin-it faster: Quadrics solve all topology optimization problems that depend
only on mass moments'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
_id: '17207'
acknowledgement: "This research was funded by the Austrian Science Fund (FWF), project
doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896
and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would
like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton
for their insightful comments on the earlier drafts, and to John Carchrae for his
valuable contribution in refining phrasing and enhancing clarity. For open access
purposes, the author has applied a CC BY public copyright license to any author-accepted
manuscript version arising from this submission."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: 'Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments:
Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587.
doi:10.1093/jeb/voae067'
apa: 'Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing
environments: Integrating theory with data. Journal of Evolutionary Biology.
Oxford University Press. https://doi.org/10.1093/jeb/voae067'
chicago: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing
Environments: Integrating Theory with Data.” Journal of Evolutionary Biology.
Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.'
ieee: 'L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments:
Integrating theory with data,” Journal of evolutionary biology, vol. 37,
no. 6. Oxford University Press, pp. 579–587, 2024.'
ista: 'Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments:
Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.'
mla: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing
Environments: Integrating Theory with Data.” Journal of Evolutionary Biology,
vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067.'
short: L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587.
date_created: 2024-07-07T22:01:04Z
date_published: 2024-06-28T00:00:00Z
date_updated: 2026-06-18T17:53:35Z
day: '28'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voae067
external_id:
isi:
- '001258359900001'
pmid:
- '38941551'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1093/jeb/voae067
month: '06'
oa: 1
oa_version: Published Version
page: 579-587
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Journal of evolutionary biology
publication_identifier:
eissn:
- 1420-9101
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Eco-evolutionary dynamics in changing environments: Integrating theory with
data'
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: 37
year: '2024'
...
---
OA_place: publisher
_id: '17208'
abstract:
- lang: eng
text: "Can current quantum computers provide a speedup over their classical counterparts
for some kinds of problems? In this thesis, with a focus on ground state search/preparation,
we address some of the challenges that both quantum annealing and variational
quantum algorithms suffer from, hindering any possible practical speedup in comparison
to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we
study the performance of quantum annealing for solving a particular combinatorial
optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem
is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$.
We consider how modifying the initial problem, by adding more interaction terms
to the corresponding Hamiltonian, leads to the emergence of a first-order phase
transition during the annealing process. This phenomenon causes the total annealing
duration, $T$, required to prepare the ground state of $H_C$ with a high probability
to increase exponentially with the size of the problem. Our findings indicate
that with the growing complexity of problem instances, the likelihood of encountering
first-order phase transitions also increases, making quantum annealing an impractical
solution for these types of combinatorial optimization problems.\r\n\r\nIn the
second part, we focus on the problem of barren plateaus in generic variational
quantum algorithms. Barren plateaus correspond to flat regions in the parameter
space where the gradient of the cost function is zero in expectation, and with
the variance decaying exponentially with the system size, thus obstructing an
efficient parameter optimization. We propose an algorithm to circumvent Barren
Plateaus by monitoring the entanglement entropy of k-local reduced density matrices,
alongside a method for estimating entanglement entropy via classical shadow tomography.
We illustrate the approach with the paradigmatic example of the variational quantum
eigensolver, and show that our algorithm effectively avoids barren plateaus in
the initialization as well as during the optimization stage. \r\n\r\nLastly, in
the last two Chapters of this thesis, we focus on the quantum approximate optimization
algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial
optimization problems in near-term quantum devices. Specifically, we focus on
how to develop rigorous initialization strategies with guarantee improvement.
Our motivation for this study lies in that for random initialization, the optimization
typically leads to local minima with poor performance. Our main result corresponds
to the analytical construction of index-1 saddle points or transition states,
stationary points with a single direction of descent, as a tool for systematically
exploring the QAOA optimization landscape. This leads us to propose a novel greedy
parameter initialization strategy that guarantees for the energy to decrease with
an increasing number of circuit layers. Furthermore, with precise estimates for
the negative Hessian eigenvalue and its eigenvector, we establish a lower bound
for energy improvement following a QAOA iteration."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
citation:
ama: Medina Ramos RA. Exploring the optimization landscape of variational quantum
algorithms. 2024. doi:10.15479/at:ista:17208
apa: Medina Ramos, R. A. (2024). Exploring the optimization landscape of variational
quantum algorithms. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17208
chicago: Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational
Quantum Algorithms.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17208.
ieee: R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum
algorithms,” Institute of Science and Technology Austria, 2024.
ista: Medina Ramos RA. 2024. Exploring the optimization landscape of variational
quantum algorithms. Institute of Science and Technology Austria.
mla: Medina Ramos, Raimel A. Exploring the Optimization Landscape of Variational
Quantum Algorithms. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17208.
short: R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum
Algorithms, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-07-09T09:14:24Z
date_published: 2024-07-09T00:00:00Z
date_updated: 2026-04-07T12:43:22Z
day: '09'
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degree_awarded: PhD
department:
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- _id: MaSe
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ec_funded: 1
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keyword:
- Quantum computing
- Variational Quantum Algorithms
- Optimization
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10545'
relation: part_of_dissertation
status: public
- id: '10067'
relation: part_of_dissertation
status: public
- id: '17222'
relation: part_of_dissertation
status: public
- id: '13125'
relation: part_of_dissertation
status: public
- id: '11471'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
title: Exploring the optimization landscape of variational quantum algorithms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
_id: '17214'
abstract:
- lang: eng
text: 'Current numerical algorithms for simulating friction fall in one of two camps:
smooth solvers sacrifice the stable treatment of static friction in exchange for
fast convergence, and non-smooth solvers accurately compute friction at convergence
rates that are often prohibitive for large graphics applications. We introduce
a novel bridge between these two ideas that computes static and dynamic friction
stably and efficiently. Our key idea is to convert the highly constrained non-smooth
problem into an unconstrained smooth problem using logarithmic barriers that converges
to the exact solution as accuracy increases. We phrase the problem as an interior
point primal-dual problem that can be solved efficiently with Newton iteration.
We observe quadratic convergence despite the non-smooth nature of the original
problem, and our method is well-suited for large systems of tightly packed objects
with many contact points. We demonstrate the efficacy of our method with stable
piles of grains and stacks of objects, complex granular flows, and robust interlocking
assemblies of rigid bodies.'
acknowledgement: We thank Vincent Acary for his help with Siconos, as well as the
anonymous reviewers and the members of the Visual Computing Group at ISTA for their
helpful comments. This research was funded in part by the European Union (ERC-2021-COG
101045083 CoDiNA).
article_processing_charge: Yes (via OA deal)
author:
- first_name: Yi-Lu
full_name: Chen, Yi-Lu
id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70
last_name: Chen
- first_name: Mickaël
full_name: Ly, Mickaël
id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1
last_name: Ly
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation.
In: Special Interest Group on Computer Graphics and Interactive Techniques
Conference Conference Papers ’24. Association for Computing Machinery; 2024.
doi:10.1145/3641519.3657485'
apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction
for rigid body animation. In Special Interest Group on Computer Graphics and
Interactive Techniques Conference Conference Papers ’24. Denver, United States:
Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485'
chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction
for Rigid Body Animation.” In Special Interest Group on Computer Graphics and
Interactive Techniques Conference Conference Papers ’24. Association for Computing
Machinery, 2024. https://doi.org/10.1145/3641519.3657485.
ieee: Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid
body animation,” in Special Interest Group on Computer Graphics and Interactive
Techniques Conference Conference Papers ’24, Denver, United States, 2024.
ista: 'Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid
body animation. Special Interest Group on Computer Graphics and Interactive Techniques
Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive
Techniques Conference.'
mla: Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.”
Special Interest Group on Computer Graphics and Interactive Techniques Conference
Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485.
short: Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics
and Interactive Techniques Conference Conference Papers ’24, Association for Computing
Machinery, 2024.
conference:
end_date: 2024-08-01
location: Denver, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2024-07-28
corr_author: '1'
date_created: 2024-07-10T11:06:20Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:54:38Z
day: '01'
ddc:
- '621'
- '531'
- '006'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3641519.3657485
external_id:
isi:
- '001282218200091'
file:
- access_level: open_access
checksum: b8b203ed09e3995ba0d7e6a76288663a
content_type: application/pdf
creator: yichen
date_created: 2024-07-10T11:03:14Z
date_updated: 2024-07-10T11:03:14Z
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content_type: video/mp4
creator: yichen
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isi: 1
keyword:
- physical simulation
- frictional contact
- rigid body mechanics
- non-smooth dynamics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: Special Interest Group on Computer Graphics and Interactive Techniques
Conference Conference Papers '24
publication_identifier:
isbn:
- '9798400705250'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Primal-dual non-smooth friction for rigid body animation
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17219'
abstract:
- lang: eng
text: 'We introduce a multi-material non-manifold mesh-based surface tracking algorithm
that converts self-intersections into topological changes. Our algorithm generalizes
prior work on manifold surface tracking with topological changes: it preserves
surface features like mesh-based methods, and it robustly handles topological
changes like level set methods. Our method also offers improved efficiency and
robustness over the state of the art. We demonstrate the effectiveness of the
approach on a range of examples, including complex soap film simulations with
thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting
of millions of triangles.'
acknowledgement: Peter Heiss-Synak helped conceive the project, helped formulate the
algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data
structure, algorithm robustness and benchmarks, helped write the paper, and provided
supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed
ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm
robustness and benchmarks, optimized the performance, produced all results, most
figures, and the supplementary video, helped write the text, and provided conceptual
solutions throughout the project. Malina Strugaru helped implement the mesh data
structure and designed re-meshing operations for non-manifold triangle meshes. Arian
Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped
write the paper. Huidong Yang developed early prototypes for isosurface extraction
and visualization. Chris Wojtan helped conceive the project, helped write the paper,
and provided supervision, prototype grid data structure code, and conceptual solutions
throughout the project. We thank the anonymous reviewers for their helpful comments,
the members of the Visual Computing Group at ISTA for their feedback, Christopher
Batty for discussions about LosTopos, and SideFX for the Houdini Education software
licenses. This research was funded in part by the European Union (ERC-2021-COG
101045083 CoDiNA).
article_number: '54'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: Irina-Malina
full_name: Strugaru, Irina-Malina
id: 2afc607f-f128-11eb-9611-8f2a0dfcf074
last_name: Strugaru
- first_name: Arian
full_name: Etemadihaghighi, Arian
id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f
last_name: Etemadihaghighi
- first_name: Huidong
full_name: Yang, Huidong
last_name: Yang
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material
mesh-based surface tracking with implicit topology changes. ACM Transactions
on Graphics. 2024;43(4). doi:10.1145/3658223
apa: Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan,
C. (2024). Multi-material mesh-based surface tracking with implicit topology changes.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223
chicago: Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong
Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit
Topology Changes.” ACM Transactions on Graphics. Association for Computing
Machinery, 2024. https://doi.org/10.1145/3658223.
ieee: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan,
“Multi-material mesh-based surface tracking with implicit topology changes,” ACM
Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery,
2024.
ista: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material
mesh-based surface tracking with implicit topology changes. ACM Transactions on
Graphics. 43(4), 54.
mla: Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit
Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association
for Computing Machinery, 2024, doi:10.1145/3658223.
short: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM
Transactions on Graphics 43 (2024).
corr_author: '1'
date_created: 2024-07-10T12:24:00Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-07T13:02:36Z
day: '01'
ddc:
- '004'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3658223
external_id:
isi:
- '001289270900021'
file:
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checksum: 1917067d4b52d7729019b03560004e43
content_type: application/pdf
creator: dernst
date_created: 2024-07-23T06:35:15Z
date_updated: 2024-07-23T06:35:15Z
file_id: '17317'
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file_size: 48763368
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success: 1
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checksum: a4f0e293184bfa034c0c585848806b17
content_type: video/mp4
creator: akalinov
date_created: 2024-07-10T12:23:44Z
date_updated: 2024-07-10T12:23:44Z
file_id: '17221'
file_name: sdtopofixer_final.mp4
file_size: 48021463
relation: main_file
success: 1
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checksum: 18fc310a78ec91651148c45a8b89fa44
content_type: application/pdf
creator: akalinov
date_created: 2025-11-11T09:50:52Z
date_updated: 2025-11-11T09:50:52Z
file_id: '20633'
file_name: SuperDuperTopoFixer.pdf
file_size: 48639581
relation: preprint
title: Authors' version of the text
file_date_updated: 2025-11-11T09:50:52Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '4'
keyword:
- surface tracking
- topology change
- non- manifold meshes
- multi-material flows
- solid modeling
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '19630'
relation: dissertation_contains
status: public
- id: '18301'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Multi-material mesh-based surface tracking with implicit topology changes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2024'
...
---
OA_place: repository
_id: '17222'
abstract:
- lang: eng
text: "The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto
implement a variational method with $2p$ layers of alternating unitary\r\noperators,
optimized by a classical computer to minimize a cost function. While\r\nrigorous
performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior
at large depths remains less clear, though simulations suggest\r\nexponentially
fast convergence for certain problems. In this work, we gain\r\ninsights into
the deep QAOA using an analytic expansion of the cost function\r\naround transition
states. Transition states are constructed in a recursive\r\nmanner: from the local
minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA
with $p+1$ layers, which are stationary points characterized\r\nby a unique direction
of negative curvature. We construct an analytic estimate\r\nof the negative curvature
and the corresponding direction in parameter space at\r\neach transition state.
The expansion of the QAOA cost function along the\r\nnegative direction to the
quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We
provide physical intuition behind the analytic\r\nexpressions for the local curvature
and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy
of our approximations and reveals that\r\nthe obtained bound and the true value
of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with
the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study
establishes an analytical method for\r\nrecursively studying the QAOA that is
applicable in the regime of high circuit\r\ndepth."
article_number: '2405.10125'
article_processing_charge: No
arxiv: 1
author:
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement
of the quantum approximate optimization algorithm. arXiv. doi:10.48550/arXiv.2405.10125
apa: Medina Ramos, R. A., & Serbyn, M. (n.d.). A recursive lower bound on the
energy improvement of the quantum approximate optimization algorithm. arXiv.
https://doi.org/10.48550/arXiv.2405.10125
chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on
the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2405.10125.
ieee: R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement
of the quantum approximate optimization algorithm,” arXiv. .
ista: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement
of the quantum approximate optimization algorithm. arXiv, 2405.10125.
mla: Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the
Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv,
2405.10125, doi:10.48550/arXiv.2405.10125.
short: R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-07-10T13:12:09Z
date_published: 2024-05-16T00:00:00Z
date_updated: 2026-04-07T12:43:22Z
day: '16'
department:
- _id: MaSe
doi: 10.48550/arXiv.2405.10125
external_id:
arxiv:
- '2405.10125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.10125
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
- id: '17208'
relation: dissertation_contains
status: public
status: public
title: A recursive lower bound on the energy improvement of the quantum approximate
optimization algorithm
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
APC_amount: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17232'
abstract:
- lang: eng
text: "The lineage relationship of clonally-related cells offers important insights
into the ontogeny and cytoarchitecture of the brain in health and disease. Here,
we provide a protocol to concurrently assess cell lineage relationship and cell-type
identity among clonally-related cells in situ. We first describe the preparation
and screening of acute brain slices containing clonally-related cells labeled
using mosaic analysis with double markers (MADM). We then outline steps to collect
RNA from individual cells for downstream applications and cell-type identification
using RNA sequencing.\r\nFor complete details on the use and execution of this
protocol, please refer to Cheung et al.\r\n1"
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: PreCl
acknowledgement: We thank R. Beattie and T. Asenov for designing and producing components
of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment
access. We thank C. Streicher and A. Heger for mouse breeding support. This work
was supported by the Scientific Service Units of IST Austria through resources provided
by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received
funding from the European Commission (IST plus postdoctoral fellowship) and S.H.
was funded by ISTA institutional funds and the Austrian Science Fund Special Research
Programmes (FWF SFB-F78 Neuro Stem Modulation).
article_number: '103168'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell
lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168
apa: Cheung, G. T., Pauler, F., Koppensteiner, P., & Hippenmeyer, S. (2024).
Protocol for mapping cell lineage and cell-type identity of clonally-related cells
in situ using MADM-CloneSeq. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168
chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer.
“Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related
Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168.
ieee: G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for
mapping cell lineage and cell-type identity of clonally-related cells in situ
using MADM-CloneSeq,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024.
ista: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping
cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
STAR Protocols. 5(3), 103168.
mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type
Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols,
vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168.
short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols
5 (2024).
corr_author: '1'
date_created: 2024-07-14T22:01:10Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:12Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
- _id: PreCl
doi: 10.1016/j.xpro.2024.103168
external_id:
pmid:
- '38968076'
file:
- access_level: open_access
checksum: 464f52ecc6ec92f509552823bb82bf79
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:16:53Z
date_updated: 2025-01-09T12:16:53Z
file_id: '18810'
file_name: 2024_STARProtoc_Cheung2.pdf
file_size: 6445556
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:16:53Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for mapping cell lineage and cell-type identity of clonally-related
cells in situ using MADM-CloneSeq
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '17233'
abstract:
- lang: eng
text: CRISPR-Cas9 technology has become an essential tool for plant genome editing.
Recent advancements have significantly improved the ability to target multiple
genes simultaneously within the same genetic background through various strategies.
Additionally, there has been significant progress in developing methods for inducible
or tissue-specific editing. These advancements offer numerous possibilities for
tailored genome modifications. Building upon existing research, we have developed
an optimized and modular strategy allowing the targeting of several genes simultaneously
in combination with the synchronized expression of the Cas9 endonuclease in the
egg cell. This system allows significant editing efficiency while avoiding mosaicism.
In addition, the versatile system we propose allows adaptation to inducible and/or
tissue-specific edition according to the promoter chosen to drive the expression
of the Cas9 gene. Here, we describe a step-by-step protocol for generating the
binary vector necessary for establishing Arabidopsis edited lines using a versatile
cloning strategy that combines Gateway® and Golden Gate technologies. We describe
a versatile system that allows the cloning of as many guides as needed to target
DNA, which can be multiplexed into a polycistronic gene and combined in the same
construct with sequences for the expression of the Cas9 endonuclease. The expression
of Cas9 is controlled by selecting from among a collection of promoters, including
constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector
containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that,
sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA
scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination
reaction is required to assemble the promoter, the zCas9 coding sequence, and
the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and
finally assembled according to the Multisite Gateway® Technology. Here, we detail
the process to express zCas9 under the control of egg cell promoter fused to enhancer
sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains
and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880
and at1g51570), using one or two sgRNA per gene.
acknowledgement: This work was supported by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING
to E.M.B.).
article_number: e5029
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziqiang
full_name: Li, Ziqiang
id: 922e68bb-1727-11ee-857c-966e8cc1b6c3
last_name: Li
- first_name: Jennifer
full_name: Huard, Jennifer
last_name: Huard
- first_name: Emmanuelle M.
full_name: Bayer, Emmanuelle M.
last_name: Bayer
- first_name: Valérie
full_name: Wattelet-Boyer, Valérie
last_name: Wattelet-Boyer
citation:
ama: LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient
multigene editing in Arabidopsis. Bio-protocol. 2024;14(13). doi:10.21769/BioProtoc.5029
apa: LI, Z., Huard, J., Bayer, E. M., & Wattelet-Boyer, V. (2024). Versatile
cloning strategy for efficient multigene editing in Arabidopsis. Bio-Protocol.
Bio-Protocol. https://doi.org/10.21769/BioProtoc.5029
chicago: LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer.
“Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol.
Bio-Protocol, 2024. https://doi.org/10.21769/BioProtoc.5029.
ieee: Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy
for efficient multigene editing in Arabidopsis,” Bio-protocol, vol. 14,
no. 13. Bio-Protocol, 2024.
ista: LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy
for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.
mla: LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing
in Arabidopsis.” Bio-Protocol, vol. 14, no. 13, e5029, Bio-Protocol, 2024,
doi:10.21769/BioProtoc.5029.
short: Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).
date_created: 2024-07-14T22:01:11Z
date_published: 2024-07-05T00:00:00Z
date_updated: 2025-03-06T10:28:18Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.21769/BioProtoc.5029
external_id:
pmid:
- '39007160'
file:
- access_level: open_access
checksum: c8671c0ad483da6407cb16cc3fef1990
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T06:16:11Z
date_updated: 2024-07-16T06:16:11Z
file_id: '17242'
file_name: 2024_BioProtocol_Li.pdf
file_size: 2896048
relation: main_file
success: 1
file_date_updated: 2024-07-16T06:16:11Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bio-protocol
publication_identifier:
eissn:
- 2331-8325
publication_status: published
publisher: Bio-Protocol
quality_controlled: '1'
scopus_import: '1'
status: public
title: Versatile cloning strategy for efficient multigene editing in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2024'
...
---
DOAJ_listed: '1'
_id: '17234'
abstract:
- lang: eng
text: The identification of red, apparently massive galaxies at z > 7 in early James
Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line
compared to standard models of galaxy growth. A major uncertainty in the interpretation
is whether the red colors are caused by evolved stellar populations, dust, or
other effects such as emission lines or active galactic nuclei (AGNs). Here we
show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent
Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer
breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4
μm and require formation histories extending hundreds of millions of years into
the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies
also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened
AGNs contribute to, or even dominate, the spectral energy distributions of these
galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii]
lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically
relaxed, inclined disks. Yet the inferred masses also remain highly uncertain.
We model the high-quality spectra using Prospector to decompose the continuum
into stellar and AGN components and explore limiting cases in stellar/AGN contribution.
This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙.
Nevertheless, all fits suggest a very early and rapid formation, most of which
follow with a truncation in star formation. Potential origins and evolutionary
tracks for these objects are discussed, from the cores of massive galaxies to
low-mass galaxies with overmassive black holes. Intriguingly, we find all of these
explanations to be incomplete; deeper and redder data are needed to understand
the physics of these systems.
acknowledgement: "We thank the anonymous referee for the helpful comments. B.W. and
J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded
by the Danish National Research Foundation (DNRF) under grant No. 140. This research
was supported by the International Space Science Institute (ISSI) in Bern, through
ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting
the James Webb Space Telescope Revolution). This work is based in part on observations
made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from
the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute,
which is operated by the Association of Universities for Research in Astronomy,
Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this
Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the
Space Telescope Science Institute. The specific observations analyzed can be accessed
via doi:10.17909/3a4n-9p88. Computations for this research were performed on the
Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar
supercomputer. This publication made use of the NASA Astrophysical Data System for
bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec).
Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle
2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib
(Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris
et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023)."
article_number: L13
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Bingjie
full_name: Wang, Bingjie
last_name: Wang
- first_name: Joel
full_name: Leja, Joel
last_name: Leja
- first_name: Anna
full_name: De Graaff, Anna
last_name: De Graaff
- first_name: Gabriel B.
full_name: Brammer, Gabriel B.
last_name: Brammer
- first_name: Andrea
full_name: Weibel, Andrea
last_name: Weibel
- first_name: Pieter
full_name: Van Dokkum, Pieter
last_name: Van Dokkum
- first_name: Josephine F.W.
full_name: Baggen, Josephine F.W.
last_name: Baggen
- first_name: Katherine A.
full_name: Suess, Katherine A.
last_name: Suess
- first_name: Jenny E.
full_name: Greene, Jenny E.
last_name: Greene
- first_name: Rachel
full_name: Bezanson, Rachel
last_name: Bezanson
- first_name: Nikko J.
full_name: Cleri, Nikko J.
last_name: Cleri
- first_name: Michaela
full_name: Hirschmann, Michaela
last_name: Hirschmann
- first_name: Ivo
full_name: Labbé, Ivo
last_name: Labbé
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Ian
full_name: Mcconachie, Ian
last_name: Mcconachie
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
- first_name: Erica
full_name: Nelson, Erica
last_name: Nelson
- first_name: Pascal A.
full_name: Oesch, Pascal A.
last_name: Oesch
- first_name: David J.
full_name: Setton, David J.
last_name: Setton
- first_name: Christina C.
full_name: Williams, Christina C.
last_name: Williams
citation:
ama: 'Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with
extended formation histories at z ∼ 7-8 in candidate massive galaxies identified
with JWST/NIRSpec. Astrophysical Journal Letters. 2024;969(1). doi:10.3847/2041-8213/ad55f7'
apa: 'Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum,
P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended
formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec.
Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad55f7'
chicago: 'Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel,
Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations
with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified
with JWST/NIRSpec.” Astrophysical Journal Letters. IOP Publishing, 2024.
https://doi.org/10.3847/2041-8213/ad55f7.'
ieee: 'B. Wang et al., “RUBIES: Evolved stellar populations with extended
formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,”
Astrophysical Journal Letters, vol. 969, no. 1. IOP Publishing, 2024.'
ista: 'Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW,
Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, Labbé I, Matthee JJ,
Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES:
Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate
massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters.
969(1), L13.'
mla: 'Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation
Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.”
Astrophysical Journal Letters, vol. 969, no. 1, L13, IOP Publishing, 2024,
doi:10.3847/2041-8213/ad55f7.'
short: B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W.
Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. Labbé,
J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C.
Williams, Astrophysical Journal Letters 969 (2024).
date_created: 2024-07-14T22:01:11Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:10:21Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.3847/2041-8213/ad55f7
external_id:
arxiv:
- '2405.01473'
isi:
- '001257903200001'
file:
- access_level: open_access
checksum: bb1a6725586df12e745d091b5778bb2b
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T06:24:29Z
date_updated: 2024-07-16T06:24:29Z
file_id: '17243'
file_name: 2024_AstrophysicalJourn_Wang.pdf
file_size: 3273303
relation: main_file
success: 1
file_date_updated: 2024-07-16T06:24:29Z
has_accepted_license: '1'
intvolume: ' 969'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Astrophysical Journal Letters
publication_identifier:
eissn:
- 2041-8213
issn:
- 2041-8205
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'RUBIES: Evolved stellar populations with extended formation histories at z
∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 969
year: '2024'
...
---
_id: '17235'
abstract:
- lang: eng
text: We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing
method to increase disorder in superconducting thin films. We study several widely
used superconductors, both single-elements and compounds. We show that ion irradiation
increases normal-state resistivity in all our films, which is expected to enable
tuning their superconducting properties, for example, toward a higher kinetic
inductance. We observe an increase in superconducting transition temperature for
Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also
improves the mixing of the two materials. We demonstrate the fabrication of an
amorphous and homogeneous film of MoSi with uniform thickness, which is promising,
for example, for superconducting nanowire single-photon detectors.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank J. A. Sauls for useful discussions. For funding of our research
project, we acknowledge the European Union’s Horizon 2020 Research and Innovation
Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED,
and ECSEL programme 101007322/MatQu. This project has also received funding from
Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291
and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish
Quantum Flagship project 359284. This work was performed as part of the Research
Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934,
and 352935). We also acknowledge funding from an internal strategic innovation project
of VTT related to the development of quantum computing technologies. This research
was supported by the Scientific Service Units of IST Austria through resources provided
by Electron Microscopy Facility. J. Senior acknowledges funding from the European
Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie
Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council
of Finland (Research Fellowship Project No. 356542).
article_number: '071101'
article_processing_charge: Yes
article_type: original
author:
- first_name: Katja
full_name: Kohopää, Katja
last_name: Kohopää
- first_name: Alberto
full_name: Ronzani, Alberto
last_name: Ronzani
- first_name: Robab Najafi
full_name: Jabdaraghi, Robab Najafi
last_name: Jabdaraghi
- first_name: Arijit
full_name: Bera, Arijit
last_name: Bera
- first_name: Mário
full_name: Ribeiro, Mário
last_name: Ribeiro
- first_name: Dibyendu
full_name: Hazra, Dibyendu
last_name: Hazra
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Mika
full_name: Prunnila, Mika
last_name: Prunnila
- first_name: Joonas
full_name: Govenius, Joonas
last_name: Govenius
- first_name: Janne S.
full_name: Lehtinen, Janne S.
last_name: Lehtinen
- first_name: Antti
full_name: Kemppinen, Antti
last_name: Kemppinen
citation:
ama: Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting
thin films. APL Materials. 2024;12(7). doi:10.1063/5.0202851
apa: Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra,
D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin
films. APL Materials. AIP Publishing. https://doi.org/10.1063/5.0202851
chicago: Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera,
Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation
on Superconducting Thin Films.” APL Materials. AIP Publishing, 2024. https://doi.org/10.1063/5.0202851.
ieee: K. Kohopää et al., “Effect of ion irradiation on superconducting thin
films,” APL Materials, vol. 12, no. 7. AIP Publishing, 2024.
ista: Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL,
Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation
on superconducting thin films. APL Materials. 12(7), 071101.
mla: Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.”
APL Materials, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:10.1063/5.0202851.
short: K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L.
Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12
(2024).
date_created: 2024-07-14T22:01:11Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:10:58Z
day: '01'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.1063/5.0202851
ec_funded: 1
external_id:
isi:
- '001260942200003'
file:
- access_level: open_access
checksum: 32a5cdf0ea9c937f806b6039f3219917
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T06:30:30Z
date_updated: 2024-07-16T06:30:30Z
file_id: '17244'
file_name: 2024_APLMaterial_Kohopaa.pdf
file_size: 9408198
relation: main_file
success: 1
file_date_updated: 2024-07-16T06:30:30Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: APL Materials
publication_identifier:
eissn:
- 2166-532X
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of ion irradiation on superconducting thin films
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17236'
abstract:
- lang: eng
text: "Currently, the best known tradeoff between approximation ratio and complexity
for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]:
it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any
ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani,
STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale,
JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity
flow problem using another application of MW. Nested MW steps are solved via a
certain \"chaining\" algorithm that combines results of multiple calls to the
maxflow algorithm.\r\nWe present an alternative approach that avoids solving the
multicommodity flow problem and instead computes \"violating paths\". This simplifies
Sherman's algorithm by removing a need for a nested application of MW, and also
allows parallelization: we show how to compute O(√(log n)/ε)-approximation via
O(logO(1) n) maxflows using O(nε) processors.\r\nWe also revisit Sherman's chaining
algorithm, and present a simpler version together with a new analysis."
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm
for sparsest cut. In: Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures. Association for Computing Machinery; 2024:403-414.
doi:10.1145/3626183.3659969'
apa: 'Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation
algorithm for sparsest cut. In Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures (pp. 403–414). Nantes, France: Association
for Computing Machinery. https://doi.org/10.1145/3626183.3659969'
chicago: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation
Algorithm for Sparsest Cut.” In Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures, 403–14. Association for Computing Machinery,
2024. https://doi.org/10.1145/3626183.3659969.
ieee: V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm
for sparsest cut,” in Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures, Nantes, France, 2024, pp. 403–414.
ista: 'Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation
algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms
and Architectures, 403–414.'
mla: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation
Algorithm for Sparsest Cut.” Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2024,
pp. 403–14, doi:10.1145/3626183.3659969.
short: V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2024, pp.
403–414.
conference:
end_date: 2024-06-21
location: Nantes, France
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2024-06-17
corr_author: '1'
date_created: 2024-07-14T22:01:11Z
date_published: 2024-06-17T00:00:00Z
date_updated: 2026-01-21T09:46:25Z
day: '17'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1145/3626183.3659969
external_id:
arxiv:
- '2307.00115'
isi:
- '001253331900044'
file:
- access_level: open_access
checksum: 6ca18ac8508719dbd5d5735f4c991af2
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T06:38:08Z
date_updated: 2024-07-16T06:38:08Z
file_id: '17245'
file_name: 2024_SPAA_Kolmogorov.pdf
file_size: 1116166
relation: main_file
success: 1
file_date_updated: 2024-07-16T06:38:08Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 403-414
publication: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and
Architectures
publication_identifier:
isbn:
- '9798400704161'
issn:
- 1548-6109
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '21007'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: A simpler and parallelizable O(√log n)-approximation algorithm for sparsest
cut
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17237'
abstract:
- lang: eng
text: 'The impact of climate change on populations will be contingent upon their
contemporary adaptive evolution. In this study, we investigated the contemporary
evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing
their spatial and temporal genomic variations using ddRAD-sequencing. These populations
were sampled from the center to the southern margin of its north-eastern Atlantic
distribution at 2 time points, spanning at least 2 generations. Through genome
scans for local adaptation at a single time point, we identified candidate loci
that showed clinal variation correlated with changes in sea surface temperature
(SST) along latitudinal gradients. This finding suggests that SST may drive the
adaptive response of these kelp populations, although factors such as species’
demographic history should also be considered. Additionally, we performed a simulation
approach to distinguish the effect of selection from genetic drift in allele frequency
changes over time. This enabled the detection of loci in the southernmost population
that exhibited temporal differentiation beyond what would be expected from genetic
drift alone: these are candidate loci which could have evolved under selection
over time. In contrast, we did not detect any outlier locus based on temporal
differentiation in the population from the North Sea, which also displayed low
and decreasing levels of genetic diversity. The diverse evolutionary scenarios
observed among populations can be attributed to variations in the prevalence of
selection relative to genetic drift across different environments. Therefore,
our study highlights the potential of temporal genomics to offer valuable insights
into the contemporary evolution of marine foundation species facing climate change.'
acknowledgement: "This work was funded by the EU project MARFOR Biodiversa/004/2015.
L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS
Foundation. The project leading to this publication has received funding from the
EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis
work is especially dedicated to the memory of Gernot Glöckner who contributed to
the sequencing of Laminaria digitata genome and passed away in very recent time.
The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr)
for providing the HPC resources that contributed to the search results reported
in this document. We also acknowledge the staff of the “Cluster de calcul intensif
HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS)
for providing the computing facilities."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lauric
full_name: Reynes, Lauric
last_name: Reynes
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Didier
full_name: Aurelle, Didier
last_name: Aurelle
- first_name: Stephane
full_name: Mauger, Stephane
last_name: Mauger
- first_name: Christophe
full_name: Destombe, Christophe
last_name: Destombe
- first_name: Myriam
full_name: Valero, Myriam
last_name: Valero
citation:
ama: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics
help in deciphering neutral and adaptive patterns in the contemporary evolution
of kelp populations. Journal of Evolutionary Biology. 2024;37(6):677-692.
doi:10.1093/jeb/voae048
apa: Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., & Valero,
M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns
in the contemporary evolution of kelp populations. Journal of Evolutionary
Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae048
chicago: Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe
Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and
Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” Journal
of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae048.
ieee: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero,
“Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations,” Journal of Evolutionary Biology, vol. 37,
no. 6. Oxford University Press, pp. 677–692, 2024.
ista: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal
genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692.
mla: Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive
Patterns in the Contemporary Evolution of Kelp Populations.” Journal of Evolutionary
Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:10.1093/jeb/voae048.
short: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal
of Evolutionary Biology 37 (2024) 677–692.
date_created: 2024-07-14T22:01:12Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-06-04T07:23:23Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jeb/voae048
external_id:
arxiv:
- '2404.14003'
pmid:
- '38629140'
intvolume: ' 37'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.14003
month: '06'
oa: 1
oa_version: Preprint
page: 677-692
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal genomics help in deciphering neutral and adaptive patterns in the
contemporary evolution of kelp populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2024'
...
---
_id: '17238'
abstract:
- lang: eng
text: We know that heritable variation is abundant, and that selection causes all
but the smallest populations to rapidly shift beyond their original trait distribution.
So then, what limits the range of a species? There are physical constraints and
also population genetic limits to the effectiveness of selection, ultimately set
by population size. Global adaptation, where the same genotype is favoured over
the whole range, is most efficient when based on a multitude of weakly selected
alleles and is effective even when local demes are small, provided that there
is some gene flow. In contrast, local adaptation is sensitive to gene flow and
may require alleles with substantial effect. How can populations combine the advantages
of large effective size with the ability to specialise into local niches? To what
extent does reproductive isolation help resolve this tension? I address these
questions using eco-evolutionary models of polygenic adaptation, contrasting discrete
demes with continuousspace.
acknowledgement: This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”.
I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their
helpful comments.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Limits to species’ range: The tension between local and global
adaptation. Journal of Evolutionary Biology. 2024;37(6):605-615. doi:10.1093/jeb/voae052'
apa: 'Barton, N. H. (2024). Limits to species’ range: The tension between local
and global adaptation. Journal of Evolutionary Biology. Oxford University
Press. https://doi.org/10.1093/jeb/voae052'
chicago: 'Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local
and Global Adaptation.” Journal of Evolutionary Biology. Oxford University
Press, 2024. https://doi.org/10.1093/jeb/voae052.'
ieee: 'N. H. Barton, “Limits to species’ range: The tension between local and global
adaptation,” Journal of Evolutionary Biology, vol. 37, no. 6. Oxford University
Press, pp. 605–615, 2024.'
ista: 'Barton NH. 2024. Limits to species’ range: The tension between local and
global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.'
mla: 'Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and
Global Adaptation.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford
University Press, 2024, pp. 605–15, doi:10.1093/jeb/voae052.'
short: N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615.
corr_author: '1'
date_created: 2024-07-14T22:01:12Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-08T08:08:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voae052
external_id:
isi:
- '001225323900001'
pmid:
- '38683160'
file:
- access_level: open_access
checksum: 94e6b68bddf6cadcec29c7f41647359f
content_type: application/pdf
creator: dernst
date_created: 2024-07-15T09:45:25Z
date_updated: 2024-07-15T09:45:25Z
file_id: '17241'
file_name: 2024_JourEvolutionaryBiology_Barton.pdf
file_size: 1194263
relation: main_file
success: 1
file_date_updated: 2024-07-15T09:45:25Z
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intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 605-615
pmid: 1
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Limits to species'' range: The tension between local and global adaptation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17239'
abstract:
- lang: eng
text: Collagen is the most abundant protein in tissue scaffolds in live organisms.
Collagen can self-assemble in vitro, which has led to a number of biotechnological
and biomedical applications. To understand the dominant factors that participate
in the formation of collagen nanostructures, here we study in real time and with
nanoscale resolution the disassembly and reassembly of collagens. We implement
a high-speed force microscope, which provides in situ high spatiotemporal resolution
images of collagen nanostructures under changing pH conditions. The disassembly
and reassembly are dominated by the electrostatic interactions among amino-acid
residues of different molecules. Acidic conditions favor disassembly by neutralizing
negatively charged residues. The process sets a net repulsive force between collagen
molecules. A neutral pH favors the presence of negative and positively charged
residues along the collagen molecules, which promotes their electrostatic attraction.
Molecular dynamics simulations reproduce the experimental behavior and validate
the electrostatic-based model of the disassembly and reassembly processes.
acknowledgement: We are grateful to Nancy Forde (Simon Fraser University) for her
motivating comments. Financial support from the Ministerio de Ciencia, Innovación
y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged.
A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship
and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant
No. 585 80296).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Clara
full_name: Garcia-Sacristan, Clara
last_name: Garcia-Sacristan
- first_name: Victor G.
full_name: Gisbert, Victor G.
last_name: Gisbert
- first_name: Kevin
full_name: Klein, Kevin
id: 1e7ede04-9e54-11f0-9ec4-8d4d5563c398
last_name: Klein
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ricardo
full_name: Garcia, Ricardo
last_name: Garcia
citation:
ama: Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging
electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS
Nano. 2024;18(28):18485-18492. doi:10.1021/acsnano.4c03839
apa: Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., & Garcia, R.
(2024). In operando imaging electrostatic-driven disassembly and reassembly of
collagen nanostructures. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.4c03839
chicago: Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić,
and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and
Reassembly of Collagen Nanostructures.” ACS Nano. American Chemical Society,
2024. https://doi.org/10.1021/acsnano.4c03839.
ieee: C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In
operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,”
ACS Nano, vol. 18, no. 28. American Chemical Society, pp. 18485–18492,
2024.
ista: Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando
imaging electrostatic-driven disassembly and reassembly of collagen nanostructures.
ACS Nano. 18(28), 18485–18492.
mla: Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly
and Reassembly of Collagen Nanostructures.” ACS Nano, vol. 18, no. 28,
American Chemical Society, 2024, pp. 18485–92, doi:10.1021/acsnano.4c03839.
short: C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano
18 (2024) 18485–18492.
date_created: 2024-07-14T22:01:12Z
date_published: 2024-07-16T00:00:00Z
date_updated: 2025-12-16T09:01:10Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1021/acsnano.4c03839
ec_funded: 1
external_id:
isi:
- '001263155500001'
pmid:
- '38958189'
file:
- access_level: open_access
checksum: b7e9ce718e92f568bcb3810e8e28e458
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:06:48Z
date_updated: 2025-01-09T12:06:48Z
file_id: '18808'
file_name: 2024_ACSNano_GarciaSacristan.pdf
file_size: 10036838
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:06:48Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '28'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 18485-18492
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: In operando imaging electrostatic-driven disassembly and reassembly of collagen
nanostructures
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: 18
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17269'
abstract:
- lang: eng
text: The directed migration of epithelial cell collectives through coordinated
movements plays a crucial role in various physiological processes and is increasingly
understood at the level of large confluent monolayers. However, numerous processes
rely on the migration of small groups of polarized epithelial clusters in complex
environments, and their responses to external geometries remain poorly understood.
To address this, we cultivate primary epithelial keratocyte tissues on adhesive
microstripes to create autonomous epithelial clusters with well-defined geometries.
We show that their migration efficiency is strongly influenced by the contact
geometry and the orientation of cell–cell contacts with respect to the direction
of migration. A combination of velocity and polarity alignment with contact regulation
of locomotion in an active matter model captures quantitatively the experimental
data. Furthermore, we predict that this combination of rules enables efficient
navigation in complex geometries, which we confirm experimentally. Altogether,
our findings provide a conceptual framework for extracting the interaction rules
of active systems from their interaction with physical boundaries, as well as
design principles for collective navigation in complex microenvironments.
acknowledgement: M.L., E.V. and S.G. acknowledge funding from the European Regional
Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the
Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS;
Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23),
the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE
project, which is financially supported by Interreg France-Wallonie-Vlaanderen,
ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow
(Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively.
E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund
for Research Training in Industry and Agriculture (FRIA). This project was supported
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie
Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS
foundation as a NOMIS fellow and by the European Molecular Biology Organization
(Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen
Center for Physics, which is supported by the National Science Foundation (Grant
No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia
(Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for
Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research
Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the
European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation
and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the
Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient
of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade
and Business.
article_processing_charge: No
article_type: original
author:
- first_name: Eléonore
full_name: Vercruysse, Eléonore
last_name: Vercruysse
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Manuel
full_name: Gómez-González, Manuel
last_name: Gómez-González
- first_name: Alexandre
full_name: Remson, Alexandre
last_name: Remson
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Yohalie
full_name: Kalukula, Yohalie
last_name: Kalukula
- first_name: Leone
full_name: Rossetti, Leone
last_name: Rossetti
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- 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: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration
efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500.
doi:10.1038/s41567-024-02532-x
apa: Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M.,
Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous
epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x
chicago: Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre
Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard
B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous
Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x.
ieee: E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous
epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp.
1492–1500, 2024.
ista: Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula
Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration
efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.
mla: Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous
Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024,
pp. 1492–500, doi:10.1038/s41567-024-02532-x.
short: E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y.
Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20
(2024) 1492–1500.
corr_author: '1'
date_created: 2024-07-16T12:32:17Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T08:28:31Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-024-02532-x
ec_funded: 1
external_id:
isi:
- '001250246200004'
intvolume: ' 20'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.07.17.500364
month: '09'
oa: 1
oa_version: Preprint
page: 1492-1500
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/a-railroad-of-cells/
scopus_import: '1'
status: public
title: Geometry-driven migration efficiency of autonomous epithelial cell clusters
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17277'
abstract:
- lang: eng
text: "This paper is devoted to stability results for the Gaussian logarithmic Sobolev
inequality, with explicit stability constants.\r\n\r\n"
acknowledgement: The authors thank Max Fathi and Pierre Cardaliaguet for fruitful
discussions and Emanuel Indrei for stimulating interactions. They also thank an
anonymous referee for useful comments and suggestions which have led to an improvement
of the manuscript. They also want to express their gratitude to the managing editor,
L. Gross, for his encouragements and questions. G.B. has been funded by the European
Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie
grant agreement No 754362. This work has been (partially) supported by the Project
Conviviality ANR-23-CE40-0003 of the French National Research Agency.
article_number: '110562'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giovanni
full_name: Brigati, Giovanni
id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1
last_name: Brigati
- first_name: Jean
full_name: Dolbeault, Jean
last_name: Dolbeault
- first_name: Nikita
full_name: Simonov, Nikita
last_name: Simonov
citation:
ama: Brigati G, Dolbeault J, Simonov N. Stability for the logarithmic Sobolev inequality.
Journal of Functional Analysis. 2024;287(8). doi:10.1016/j.jfa.2024.110562
apa: Brigati, G., Dolbeault, J., & Simonov, N. (2024). Stability for the logarithmic
Sobolev inequality. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110562
chicago: Brigati, Giovanni, Jean Dolbeault, and Nikita Simonov. “Stability for the
Logarithmic Sobolev Inequality.” Journal of Functional Analysis. Elsevier,
2024. https://doi.org/10.1016/j.jfa.2024.110562.
ieee: G. Brigati, J. Dolbeault, and N. Simonov, “Stability for the logarithmic Sobolev
inequality,” Journal of Functional Analysis, vol. 287, no. 8. Elsevier,
2024.
ista: Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev
inequality. Journal of Functional Analysis. 287(8), 110562.
mla: Brigati, Giovanni, et al. “Stability for the Logarithmic Sobolev Inequality.”
Journal of Functional Analysis, vol. 287, no. 8, 110562, Elsevier, 2024,
doi:10.1016/j.jfa.2024.110562.
short: G. Brigati, J. Dolbeault, N. Simonov, Journal of Functional Analysis 287
(2024).
corr_author: '1'
date_created: 2024-07-21T22:01:00Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2025-09-08T08:25:34Z
day: '15'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2024.110562
external_id:
arxiv:
- '2303.12926'
isi:
- '001271814000001'
intvolume: ' 287'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 10.48550/arXiv.2303.12926
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability for the logarithmic Sobolev inequality
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...