---
_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
file_id: '17215'
file_name: sig24_friction_authors.pdf
file_size: 47309472
relation: main_file
success: 1
- access_level: open_access
checksum: 89d81b397b4b6469d828808a68b70820
content_type: application/pdf
creator: yichen
date_created: 2024-07-10T11:03:12Z
date_updated: 2024-07-10T11:03:12Z
file_id: '17216'
file_name: sig24_friction_supplementary.pdf
file_size: 10518286
relation: main_file
success: 1
- access_level: open_access
checksum: 7123deed34a5456810e7b5336a31c657
content_type: video/mp4
creator: yichen
date_created: 2024-07-10T11:03:51Z
date_updated: 2024-07-10T11:03:51Z
file_id: '17217'
file_name: friction_paper_extra_video_finished.mp4
file_size: 71789192
relation: main_file
success: 1
- access_level: open_access
checksum: e606fc1ae8f2610ce3b4421566800b45
content_type: video/mp4
creator: yichen
date_created: 2024-07-10T11:03:58Z
date_updated: 2024-07-10T11:03:58Z
file_id: '17218'
file_name: friction_paper_video_finished.mp4
file_size: 280610763
relation: main_file
success: 1
file_date_updated: 2024-07-10T11:03:58Z
has_accepted_license: '1'
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:
- access_level: open_access
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'
file_name: 2024_ACMToG_HeissSynak.pdf
file_size: 48763368
relation: main_file
success: 1
- access_level: open_access
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
- access_level: open_access
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
license: https://creativecommons.org/licenses/by/4.0/
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'
...
---
OA_type: free access
_id: '17231'
abstract:
- lang: eng
text: In the class of projective billiards, which contains the usual billiards,
we exhibit counter-examples to Ivrii's conjecture, which states that in any planar
billiard with smooth boundary the set of periodic orbits has zero measure. The
counter-examples are polygons admitting a 2-parameters family of n-periodic orbits,
with n being either 3 or any even integer greater than 4.
article_processing_charge: No
article_type: original
author:
- first_name: Corentin
full_name: Fiorebe, Corentin
id: 06619f18-9070-11eb-847d-d1ee780bd88b
last_name: Fiorebe
citation:
ama: Fiorebe C. Examples of projective billiards with open sets of periodic orbits.
Discrete and Continuous Dynamical Systems- Series A. 2024;44(11):3287-3301.
doi:10.3934/dcds.2024059
apa: Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic
orbits. Discrete and Continuous Dynamical Systems- Series A. American Institute
of Mathematical Sciences. https://doi.org/10.3934/dcds.2024059
chicago: Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of
Periodic Orbits.” Discrete and Continuous Dynamical Systems- Series A.
American Institute of Mathematical Sciences, 2024. https://doi.org/10.3934/dcds.2024059.
ieee: C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,”
Discrete and Continuous Dynamical Systems- Series A, vol. 44, no. 11. American
Institute of Mathematical Sciences, pp. 3287–3301, 2024.
ista: Fiorebe C. 2024. Examples of projective billiards with open sets of periodic
orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301.
mla: Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic
Orbits.” Discrete and Continuous Dynamical Systems- Series A, vol. 44,
no. 11, American Institute of Mathematical Sciences, 2024, pp. 3287–301, doi:10.3934/dcds.2024059.
short: C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024)
3287–3301.
corr_author: '1'
date_created: 2024-07-14T22:01:10Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2026-06-18T17:54:16Z
day: '01'
ddc:
- '500'
department:
- _id: VaKa
doi: 10.3934/dcds.2024059
external_id:
isi:
- '001230091000001'
intvolume: ' 44'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3934/dcds.2024059
month: '11'
oa: 1
oa_version: Published Version
page: 3287-3301
publication: Discrete and Continuous Dynamical Systems- Series A
publication_identifier:
eissn:
- 1553-5231
issn:
- 1078-0947
publication_status: published
publisher: American Institute of Mathematical Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Examples of projective billiards with open sets of periodic orbits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
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
has_accepted_license: '1'
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'
...
---
_id: '17278'
abstract:
- lang: eng
text: An azeotrope is a constant boiling point mixture, and its behavior is important
for fluid separation processes. Predicting azeotropes from atomistic simulations
is difficult due to the complexities and convergence problems of Monte Carlo and
free-energy perturbation techniques. Here, we present a methodology for predicting
the azeotropes of binary mixtures, which computes the compositional dependence
of chemical potentials from molecular dynamics simulations using the S0 method
and employs experimental boiling point and vaporization enthalpy data. Using this
methodology, we reproduce the azeotropes, or lack thereof, in five case studies,
including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and
acetone/chloroform mixtures. We find that it is crucial to use the experimental
boiling point and vaporization enthalpy for reliable azeotrope predictions, as
empirical force fields are not accurate enough for these quantities. Finally,
we use regular solution models to rationalize the azeotropes and reveal that they
tend to form when the mixture components have similar boiling points and strong
interactions.
acknowledgement: B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope
and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek
for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge
the resources provided by the Cambridge Tier-2 system operated by the University
of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No.
EP/P020259/1).
article_number: '034111'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xiaoyu
full_name: Wang, Xiaoyu
id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
last_name: Wang
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Wang X, Cheng B. Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures. Journal of Chemical Physics.
2024;161(3). doi:10.1063/5.0217232
apa: Wang, X., & Cheng, B. (2024). Integrating molecular dynamics simulations
and experimental data for azeotrope predictions in binary mixtures. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0217232
chicago: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal
of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0217232.
ieee: X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures,” Journal of Chemical Physics,
vol. 161, no. 3. AIP Publishing, 2024.
ista: Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental
data for azeotrope predictions in binary mixtures. Journal of Chemical Physics.
161(3), 034111.
mla: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal
of Chemical Physics, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:10.1063/5.0217232.
short: X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:00Z
date_published: 2024-07-14T00:00:00Z
date_updated: 2025-09-08T08:26:09Z
day: '14'
department:
- _id: BiCh
- _id: GradSch
doi: 10.1063/5.0217232
external_id:
arxiv:
- '2405.02216'
isi:
- '001281819100016'
pmid:
- '39007379'
intvolume: ' 161'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.02216
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0
scopus_import: '1'
status: public
title: Integrating molecular dynamics simulations and experimental data for azeotrope
predictions in binary mixtures
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 161
year: '2024'
...
---
_id: '17279'
abstract:
- lang: eng
text: In a recent issue of Cell, Zhang et al.1 demonstrate that mechanical features
of a solid tumor can drive T cells into dysfunctionality and identify pathways
that revert this “exhausted” state.
article_processing_charge: No
article_type: review
author:
- first_name: Mario
full_name: Avellaneda Sarrió, Mario
id: DC4BA84C-56E6-11EA-AD5D-348C3DDC885E
last_name: Avellaneda Sarrió
orcid: 0000-0001-6406-524X
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Avellaneda Sarrió M, Sixt MK. Rescuing T cells from stiff tumors. Cell Chemical
Biology. 2024;31(7):1242-1243. doi:10.1016/j.chembiol.2024.06.011
apa: Avellaneda Sarrió, M., & Sixt, M. K. (2024). Rescuing T cells from stiff
tumors. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2024.06.011
chicago: Avellaneda Sarrió, Mario, and Michael K Sixt. “Rescuing T Cells from Stiff
Tumors.” Cell Chemical Biology. Elsevier, 2024. https://doi.org/10.1016/j.chembiol.2024.06.011.
ieee: M. Avellaneda Sarrió and M. K. Sixt, “Rescuing T cells from stiff tumors,”
Cell Chemical Biology, vol. 31, no. 7. Elsevier, pp. 1242–1243, 2024.
ista: Avellaneda Sarrió M, Sixt MK. 2024. Rescuing T cells from stiff tumors. Cell
Chemical Biology. 31(7), 1242–1243.
mla: Avellaneda Sarrió, Mario, and Michael K. Sixt. “Rescuing T Cells from Stiff
Tumors.” Cell Chemical Biology, vol. 31, no. 7, Elsevier, 2024, pp. 1242–43,
doi:10.1016/j.chembiol.2024.06.011.
short: M. Avellaneda Sarrió, M.K. Sixt, Cell Chemical Biology 31 (2024) 1242–1243.
corr_author: '1'
date_created: 2024-07-21T22:01:00Z
date_published: 2024-07-18T00:00:00Z
date_updated: 2025-09-08T08:27:03Z
day: '18'
department:
- _id: MiSi
doi: 10.1016/j.chembiol.2024.06.011
external_id:
isi:
- '001275725000001'
pmid:
- '39029454'
intvolume: ' 31'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1242-1243
pmid: 1
publication: Cell Chemical Biology
publication_identifier:
eissn:
- 2451-9448
issn:
- 2451-9456
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rescuing T cells from stiff tumors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17280'
abstract:
- lang: eng
text: Adherens junction–associated protein 1 (AJAP1) has been implicated in brain
diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely
expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs),
which inhibit neurotransmitter release at most synapses in the brain. Here, we
show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits
GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several
monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental
disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs,
resulting in the inability to recruit them. Ultrastructural analysis revealed
significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice.
Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition
at excitatory and inhibitory synapses, along with impaired synaptic plasticity.
Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level
of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function
AJAP1 variants.
acknowledgement: "Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration
with Pawel Pelczar at the center for transgenic models at the University of Basel,
Switzerland. We thank the imaging core facility (IMCF, University of Basel) and
in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM
microscope.\r\nThis work was supported by a grant from the Swiss National Science
Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and
E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1,
16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative
Medicines Initiatives from the European Commission joint undertaking under grant
agreement No 777394."
article_number: adk5462
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Früh, Simon
last_name: Früh
- first_name: Sami
full_name: Boudkkazi, Sami
last_name: Boudkkazi
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Vita
full_name: Sereikaite, Vita
last_name: Sereikaite
- first_name: Li Yuan
full_name: Chen, Li Yuan
last_name: Chen
- first_name: Diego
full_name: Fernandez-Fernandez, Diego
last_name: Fernandez-Fernandez
- first_name: Pascal D.
full_name: Rem, Pascal D.
last_name: Rem
- first_name: Daniel
full_name: Ulrich, Daniel
last_name: Ulrich
- first_name: Jochen
full_name: Schwenk, Jochen
last_name: Schwenk
- first_name: Ziyang
full_name: Chen, Ziyang
last_name: Chen
- first_name: Elodie Le
full_name: Monnier, Elodie Le
last_name: Monnier
- first_name: Thorsten
full_name: Fritzius, Thorsten
last_name: Fritzius
- first_name: Sabrina M.
full_name: Innocenti, Sabrina M.
last_name: Innocenti
- first_name: Valérie
full_name: Besseyrias, Valérie
last_name: Besseyrias
- first_name: Luca
full_name: Trovò, Luca
last_name: Trovò
- first_name: Michal
full_name: Stawarski, Michal
last_name: Stawarski
- first_name: Emanuela
full_name: Argilli, Emanuela
last_name: Argilli
- first_name: Elliott H.
full_name: Sherr, Elliott H.
last_name: Sherr
- first_name: Bregje
full_name: Van Bon, Bregje
last_name: Van Bon
- first_name: Erik Jan
full_name: Kamsteeg, Erik Jan
last_name: Kamsteeg
- first_name: Maria
full_name: Iascone, Maria
last_name: Iascone
- first_name: Alba
full_name: Pilotta, Alba
last_name: Pilotta
- first_name: Maria R.
full_name: Cutrì, Maria R.
last_name: Cutrì
- first_name: Mahshid S.
full_name: Azamian, Mahshid S.
last_name: Azamian
- first_name: Andrés
full_name: Hernández-García, Andrés
last_name: Hernández-García
- first_name: Seema R.
full_name: Lalani, Seema R.
last_name: Lalani
- first_name: Jill A.
full_name: Rosenfeld, Jill A.
last_name: Rosenfeld
- first_name: Xiaonan
full_name: Zhao, Xiaonan
last_name: Zhao
- first_name: Tiphanie P.
full_name: Vogel, Tiphanie P.
last_name: Vogel
- first_name: Herda
full_name: Ona, Herda
last_name: Ona
- first_name: Daryl A.
full_name: Scott, Daryl A.
last_name: Scott
- first_name: Peter
full_name: Scheiffele, Peter
last_name: Scheiffele
- first_name: Kristian
full_name: Strømgaard, Kristian
last_name: Strømgaard
- first_name: Mehdi
full_name: Tafti, Mehdi
last_name: Tafti
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
citation:
ama: Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of-
function variants disrupt trans-synaptic control of neurotransmitter release.
Science Advances. 2024;10(28). doi:10.1126/sciadv.adk5462
apa: Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez,
D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants
disrupt trans-synaptic control of neurotransmitter release. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk5462
chicago: Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan
Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1
Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter
Release.” Science Advances. American Association for the Advancement of
Science, 2024. https://doi.org/10.1126/sciadv.adk5462.
ieee: S. Früh et al., “Monoallelic de novo AJAP1 loss-of- function variants
disrupt trans-synaptic control of neurotransmitter release,” Science Advances,
vol. 10, no. 28. American Association for the Advancement of Science, 2024.
ista: Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez
D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM,
Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ,
Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld
JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann
M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of-
function variants disrupt trans-synaptic control of neurotransmitter release.
Science Advances. 10(28), adk5462.
mla: Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt
Trans-Synaptic Control of Neurotransmitter Release.” Science Advances,
vol. 10, no. 28, adk5462, American Association for the Advancement of Science,
2024, doi:10.1126/sciadv.adk5462.
short: S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez,
P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti,
V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J.
Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García,
S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele,
K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science
Advances 10 (2024).
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-12T00:00:00Z
date_updated: 2025-09-08T08:15:54Z
day: '12'
ddc:
- '570'
department:
- _id: RySh
- _id: PreCl
doi: 10.1126/sciadv.adk5462
external_id:
isi:
- '001280159000022'
pmid:
- '38985877'
file:
- access_level: open_access
checksum: 9cbc4501fcd4ba1c0811fd244031422b
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:29:27Z
date_updated: 2024-07-22T06:29:27Z
file_id: '17287'
file_name: 2024_ScienceAdv_Früh.pdf
file_size: 7241489
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:29:27Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '28'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic
control of neurotransmitter release
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: 10
year: '2024'
...
---
_id: '17281'
abstract:
- lang: eng
text: We extend the free convolution of Brown measures of R-diagonal elements introduced
by Kösters and Tikhomirov [ 28] to fractional powers. We then show how this fractional
free convolution arises naturally when studying the roots of random polynomials
with independent coefficients under repeated differentiation. When the proportion
of derivatives to the degree approaches one, we establish central limit theorem-type
behavior and discuss stable distributions.
acknowledgement: This work was supported by the National Science Foundation [Grant
No. DMS-2143142 to S.O.]; and the European Research Council [Grant No. 101020331].The
third author acknowledges the support of the University of Colorado Boulder, where
a portion of this work was completed. The authors thank Martin Auer, Vadim Gorin,
Brian Hall, and Noah Williams for comments, corrections, and references. The authors
also wish to thank the anonymous referees for useful feedback and corrections.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrew J
full_name: Campbell, Andrew J
id: 582b06a9-1f1c-11ee-b076-82ffce00dde4
last_name: Campbell
- first_name: Sean
full_name: O'Rourke, Sean
last_name: O'Rourke
- first_name: David T
full_name: Renfrew, David T
id: 4845BF6A-F248-11E8-B48F-1D18A9856A87
last_name: Renfrew
orcid: 0000-0003-3493-121X
citation:
ama: Campbell AJ, O’Rourke S, Renfrew DT. The fractional free convolution of R-diagonal
elements and random polynomials under repeated differentiation. International
Mathematics Research Notices. 2024;2024(13):10189-10218. doi:10.1093/imrn/rnae062
apa: Campbell, A. J., O’Rourke, S., & Renfrew, D. T. (2024). The fractional
free convolution of R-diagonal elements and random polynomials under repeated
differentiation. International Mathematics Research Notices. Oxford University
Press. https://doi.org/10.1093/imrn/rnae062
chicago: Campbell, Andrew J, Sean O’Rourke, and David T Renfrew. “The Fractional
Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated
Differentiation.” International Mathematics Research Notices. Oxford University
Press, 2024. https://doi.org/10.1093/imrn/rnae062.
ieee: A. J. Campbell, S. O’Rourke, and D. T. Renfrew, “The fractional free convolution
of R-diagonal elements and random polynomials under repeated differentiation,”
International Mathematics Research Notices, vol. 2024, no. 13. Oxford University
Press, pp. 10189–10218, 2024.
ista: Campbell AJ, O’Rourke S, Renfrew DT. 2024. The fractional free convolution
of R-diagonal elements and random polynomials under repeated differentiation.
International Mathematics Research Notices. 2024(13), 10189–10218.
mla: Campbell, Andrew J., et al. “The Fractional Free Convolution of R-Diagonal
Elements and Random Polynomials under Repeated Differentiation.” International
Mathematics Research Notices, vol. 2024, no. 13, Oxford University Press,
2024, pp. 10189–218, doi:10.1093/imrn/rnae062.
short: A.J. Campbell, S. O’Rourke, D.T. Renfrew, International Mathematics Research
Notices 2024 (2024) 10189–10218.
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:16:32Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1093/imrn/rnae062
external_id:
isi:
- '001198019500001'
file:
- access_level: open_access
checksum: f36a7dbf53f23d5833db711052e69b49
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T06:40:19Z
date_updated: 2024-07-22T06:40:19Z
file_id: '17288'
file_name: 2024_IMRN_Campbell.pdf
file_size: 1233508
relation: main_file
success: 1
file_date_updated: 2024-07-22T06:40:19Z
has_accepted_license: '1'
intvolume: ' 2024'
isi: 1
issue: '13'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 10189-10218
publication: International Mathematics Research Notices
publication_identifier:
eissn:
- 1687-0247
issn:
- 1073-7928
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The fractional free convolution of R-diagonal elements and random polynomials
under repeated differentiation
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: 2024
year: '2024'
...
---
_id: '17282'
abstract:
- lang: eng
text: Let X be a vector field and Y be a co-vector field on a smooth manifold M.
Does there exist a smooth Riemannian metric gαβ on M such that Yβ=gαβXα ?
The main result of this note gives necessary and sufficient conditions for this
to be true. As an application of this result we show that a finite-dimensional
ergodic Lindblad equation admits a gradient flow structure for the von Neumann
relative entropy if and only if the condition of BKM-detailed balance holds.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).J. M. gratefully acknowledges support by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 716117), and by the Austrian Science Fund (FWF), Project SFB
F65. We thank the anonymous referee for valuable comments on the paper.
article_number: '153'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Brooks M, Maas J. Characterisation of gradient flows for a given functional.
Calculus of Variations and Partial Differential Equations. 2024;63(6).
doi:10.1007/s00526-024-02755-z
apa: Brooks, M., & Maas, J. (2024). Characterisation of gradient flows for a
given functional. Calculus of Variations and Partial Differential Equations.
Springer Nature. https://doi.org/10.1007/s00526-024-02755-z
chicago: Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a
given Functional.” Calculus of Variations and Partial Differential Equations.
Springer Nature, 2024. https://doi.org/10.1007/s00526-024-02755-z.
ieee: M. Brooks and J. Maas, “Characterisation of gradient flows for a given functional,”
Calculus of Variations and Partial Differential Equations, vol. 63, no.
6. Springer Nature, 2024.
ista: Brooks M, Maas J. 2024. Characterisation of gradient flows for a given functional.
Calculus of Variations and Partial Differential Equations. 63(6), 153.
mla: Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given
Functional.” Calculus of Variations and Partial Differential Equations,
vol. 63, no. 6, 153, Springer Nature, 2024, doi:10.1007/s00526-024-02755-z.
short: M. Brooks, J. Maas, Calculus of Variations and Partial Differential Equations
63 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:24:51Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-024-02755-z
ec_funded: 1
external_id:
arxiv:
- '2209.11149'
isi:
- '001258097800003'
pmid:
- '38947856'
file:
- access_level: open_access
checksum: a0cf0e0ba2157aabb287cb597be17dac
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T07:05:32Z
date_updated: 2024-07-22T07:05:32Z
file_id: '17289'
file_name: 2024_CalculusVariations_Brooks.pdf
file_size: 416622
relation: main_file
success: 1
file_date_updated: 2024-07-22T07:05:32Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '6'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterisation of gradient flows for a given functional
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: 63
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17283'
abstract:
- lang: eng
text: 'We consider the problems of statically refuting equivalence and similarity
of output distributions defined by a pair of probabilistic programs. Equivalence
and similarity are two fundamental relational properties of probabilistic programs
that are essential for their correctness both in implementation and in compilation.
In this work, we present a new method for static equivalence and similarity refutation.
Our method refutes equivalence and similarity by computing a function over program
outputs whose expected value with respect to the output distributions of two programs
is different. The function is computed simultaneously with an upper expectation
supermartingale and a lower expectation submartingale for the two programs, which
we show to together provide a formal certificate for refuting equivalence and
similarity. To the best of our knowledge, our method is the first approach to
relational program analysis to offer the combination of the following desirable
features: (1) it is fully automated, (2) it is applicable to infinite-state probabilistic
programs, and (3) it provides formal guarantees on the correctness of its results.
We implement a prototype of our method and our experiments demonstrate the effectiveness
of our method to refute equivalence and similarity for a number of examples collected
from the literature.'
acknowledgement: "This research was partially supported by the ERC CoG 863818 (ForM-SMArt)
grant. Petr Novotný\r\nis supported by the Czech Science Foundation grant no. GA23-06963S.\r\n"
article_number: '232'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan
full_name: Kafshdar Goharshadi, Ehsan
id: 103b4fa0-896a-11ed-bdf8-87b697bef40d
last_name: Kafshdar Goharshadi
orcid: 0000-0002-8595-0587
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: Chatterjee K, Goharshady E, Novotný P, Zikelic D. Equivalence and similarity
refutation for probabilistic programs. Proceedings of the ACM on Programming
Languages. 2024;8. doi:10.1145/3656462
apa: Chatterjee, K., Goharshady, E., Novotný, P., & Zikelic, D. (2024). Equivalence
and similarity refutation for probabilistic programs. Proceedings of the ACM
on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656462
chicago: Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, and Dorde Zikelic.
“Equivalence and Similarity Refutation for Probabilistic Programs.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2024. https://doi.org/10.1145/3656462.
ieee: K. Chatterjee, E. Goharshady, P. Novotný, and D. Zikelic, “Equivalence and
similarity refutation for probabilistic programs,” Proceedings of the ACM on
Programming Languages, vol. 8. Association for Computing Machinery, 2024.
ista: Chatterjee K, Goharshady E, Novotný P, Zikelic D. 2024. Equivalence and similarity
refutation for probabilistic programs. Proceedings of the ACM on Programming Languages.
8, 232.
mla: Chatterjee, Krishnendu, et al. “Equivalence and Similarity Refutation for Probabilistic
Programs.” Proceedings of the ACM on Programming Languages, vol. 8, 232,
Association for Computing Machinery, 2024, doi:10.1145/3656462.
short: K. Chatterjee, E. Goharshady, P. Novotný, D. Zikelic, Proceedings of the
ACM on Programming Languages 8 (2024).
corr_author: '1'
date_created: 2024-07-21T22:01:01Z
date_published: 2024-06-20T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: GradSch
doi: 10.1145/3656462
ec_funded: 1
external_id:
arxiv:
- '2404.03430'
file:
- access_level: open_access
checksum: 8cbf220f284a4a87d093db5320c5afdd
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T07:17:14Z
date_updated: 2024-07-22T07:17:14Z
file_id: '17290'
file_name: 2024_ACMProgLang_Chatterjee.pdf
file_size: 355421
relation: main_file
success: 1
file_date_updated: 2024-07-22T07:17:14Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equivalence and similarity refutation for probabilistic programs
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: 8
year: '2024'
...