---
OA_place: repository
OA_type: green
_id: '21237'
abstract:
- lang: eng
text: Intelligent soft matter lies at the intersection of materials science, physics,
and cognitive science, promising to change how we design and interact with materials.
This transformative field aims to create materials with life-like capabilities,
such as perception, learning, memory, and adaptive behavior. Unlike traditional
materials, which typically perform static or predefined functions, intelligent
soft matter can dynamically interact with its environment, integrating multiple
sensory inputs, retaining past experiences, and making decisions to optimize its
responses. Inspired by biological systems, these materials leverage the inherent
properties of soft matter such as flexibility, adaptability, and responsiveness
to perform functions that mimic cognitive processes. By synthesizing current research
trends and projecting their evolution, we present a forward-looking perspective
on how intelligent soft matter could be constructed, with the aim of inspiring
innovations in areas such as biomedical devices, adaptive robotics, and beyond.
We highlight new pathways for integrating sensing, memory and actuation with low-power
internal operations, and we discuss key challenges in realizing materials that
exhibit truly “intelligent behavior”. These approaches outline a path toward more
robust, versatile, and scalable materials that can potentially act, compute, and
“think” through their inherent intrinsic material properties—moving beyond traditional
smart technologies that rely on external control.
acknowledgement: 'The work is the result of the SoftComp Topical workshop on Intelligent
Soft Matter, Salou 2025 (https://softmat.net/intelligent-soft-matter/) financed
by SoftComp Network of Excellence (https://eu-softcomp.net/). Various AI tools were
used for preparation of the manuscript: language models Google Gemini 2.0 series
and Discovery Engine (https://explore-the-unknown.vercel.app) for literature processing,
structuring contributions, finding concept overlaps and summarizing according to
procedure explained in https://github.com/vbaulin/IntelliDE/.'
article_processing_charge: No
article_type: review
author:
- first_name: Vladimir A.
full_name: Baulin, Vladimir A.
last_name: Baulin
- first_name: Achille
full_name: Giacometti, Achille
last_name: Giacometti
- first_name: Dmitry A.
full_name: Fedosov, Dmitry A.
last_name: Fedosov
- first_name: Stephen
full_name: Ebbens, Stephen
last_name: Ebbens
- first_name: Nydia R.
full_name: Varela-Rosales, Nydia R.
last_name: Varela-Rosales
- first_name: Neus
full_name: Feliu, Neus
last_name: Feliu
- first_name: Mithun
full_name: Chowdhury, Mithun
last_name: Chowdhury
- first_name: Minghan
full_name: Hu, Minghan
last_name: Hu
- first_name: Rudolf
full_name: Füchslin, Rudolf
last_name: Füchslin
- first_name: Marjolein
full_name: Dijkstra, Marjolein
last_name: Dijkstra
- first_name: Matan
full_name: Mussel, Matan
last_name: Mussel
- first_name: René
full_name: van Roij, René
last_name: van Roij
- first_name: Dong
full_name: Xie, Dong
last_name: Xie
- first_name: Vassil
full_name: Tzanov, Vassil
last_name: Tzanov
- first_name: Mengjie
full_name: Zu, Mengjie
id: 26dd9e7c-e86a-11eb-a854-82ac731c9ae2
last_name: Zu
- first_name: Samuel
full_name: Hidalgo-Caballero, Samuel
last_name: Hidalgo-Caballero
- first_name: Ye
full_name: Yuan, Ye
last_name: Yuan
- first_name: Luca
full_name: Cocconi, Luca
last_name: Cocconi
- first_name: Cheol-Min
full_name: Ghim, Cheol-Min
last_name: Ghim
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: M. Carmen
full_name: Miguel, M. Carmen
last_name: Miguel
- first_name: Maria Jose
full_name: Esplandiu, Maria Jose
last_name: Esplandiu
- first_name: Juliane
full_name: Simmchen, Juliane
last_name: Simmchen
- first_name: Wolfgang J.
full_name: Parak, Wolfgang J.
last_name: Parak
- first_name: Marco
full_name: Werner, Marco
last_name: Werner
- first_name: Gerhard
full_name: Gompper, Gerhard
last_name: Gompper
- first_name: Martin M.
full_name: Hanczyc, Martin M.
last_name: Hanczyc
citation:
ama: 'Baulin VA, Giacometti A, Fedosov DA, et al. Intelligent soft matter: Towards
embodied intelligence. Soft Matter. 2025;(21):4129-4145. doi:10.1039/d5sm00174a'
apa: 'Baulin, V. A., Giacometti, A., Fedosov, D. A., Ebbens, S., Varela-Rosales,
N. R., Feliu, N., … Hanczyc, M. M. (2025). Intelligent soft matter: Towards embodied
intelligence. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d5sm00174a'
chicago: 'Baulin, Vladimir A., Achille Giacometti, Dmitry A. Fedosov, Stephen Ebbens,
Nydia R. Varela-Rosales, Neus Feliu, Mithun Chowdhury, et al. “Intelligent Soft
Matter: Towards Embodied Intelligence.” Soft Matter. Royal Society of Chemistry,
2025. https://doi.org/10.1039/d5sm00174a.'
ieee: 'V. A. Baulin et al., “Intelligent soft matter: Towards embodied intelligence,”
Soft Matter, no. 21. Royal Society of Chemistry, pp. 4129–4145, 2025.'
ista: 'Baulin VA, Giacometti A, Fedosov DA, Ebbens S, Varela-Rosales NR, Feliu N,
Chowdhury M, Hu M, Füchslin R, Dijkstra M, Mussel M, van Roij R, Xie D, Tzanov
V, Zu M, Hidalgo-Caballero S, Yuan Y, Cocconi L, Ghim C-M, Cottin-Bizonne C, Miguel
MC, Esplandiu MJ, Simmchen J, Parak WJ, Werner M, Gompper G, Hanczyc MM. 2025.
Intelligent soft matter: Towards embodied intelligence. Soft Matter. (21), 4129–4145.'
mla: 'Baulin, Vladimir A., et al. “Intelligent Soft Matter: Towards Embodied Intelligence.”
Soft Matter, no. 21, Royal Society of Chemistry, 2025, pp. 4129–45, doi:10.1039/d5sm00174a.'
short: V.A. Baulin, A. Giacometti, D.A. Fedosov, S. Ebbens, N.R. Varela-Rosales,
N. Feliu, M. Chowdhury, M. Hu, R. Füchslin, M. Dijkstra, M. Mussel, R. van Roij,
D. Xie, V. Tzanov, M. Zu, S. Hidalgo-Caballero, Y. Yuan, L. Cocconi, C.-M. Ghim,
C. Cottin-Bizonne, M.C. Miguel, M.J. Esplandiu, J. Simmchen, W.J. Parak, M. Werner,
G. Gompper, M.M. Hanczyc, Soft Matter (2025) 4129–4145.
date_created: 2026-02-16T15:03:08Z
date_published: 2025-06-07T00:00:00Z
date_updated: 2026-02-17T11:27:48Z
day: '07'
department:
- _id: CaGo
doi: 10.1039/d5sm00174a
external_id:
pmid:
- '40358970'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.whiterose.ac.uk/id/eprint/226553/4/Perspective_v6_clean.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: 4129-4145
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Intelligent soft matter: Towards embodied intelligence'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21241'
abstract:
- lang: eng
text: White dwarfs (WDs) showing transits from orbiting planetary debris provide
significant insights into the structure and dynamics of debris disks, which are
eventually accreted to produce metal pollution. This is a rare class of objects
with only eight published systems. In this work, we perform a systematic search
for such systems within 500 pc in the Gaia-eDR3 catalog of WDs using the light
curves from the Zwicky Transient Facility (ZTF) and present six new candidates.
Our selection process targets the top 1% most photometrically variable sources
identified using a combined variability metric from ZTF and Gaia eDR3 photometry,
boosted by a metric space we define using von Neumann statistics and Pearson-Skew
as a novel discovery tool to identify these systems. This is followed by optical
spectroscopic observations of visually selected variables to confirm metal pollution.
Four of the six systems show long-timescale photometric variability spanning several
months to years, resulting either from long-term evolution of transit activity
or dust and debris clouds at wide orbits. Among them, WD J1013–0427 shows an indication
of reddening during the long-duration dip. Interpreting this as dust extinction
makes it the first system to indicate an abundance of dust grains with radius
≲0.3 μm in the occulting material. The same object also shows metal emission lines
that map an optically thick eccentric gas disk orbiting within the star’s Roche
limit. For each candidate, we infer the abundances of the photospheric metals
and estimate accretion rates. We show that transiting debris systems tend to have
higher inferred accretion rates compared to the general population of metal-polluted
WDs. Growing the number of these systems will further illuminate such comparative
properties in the near future. Separately, we also serendipitously discovered
an AM Canis Venaticorum showing a very long-duration outburst—only the fourth
such system to be known.
acknowledgement: "This work is based on observations obtained with the Samuel Oschin
Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory as part of
the Zwicky Transient Facility project. Z.T.F. is supported by the National Science
Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration including
current partners Caltech, IPAC, the Oskar Klein Center at Stockholm University,
the University of Maryland, University of California, Berkeley, the University of
Wisconsin at Milwaukee, University of Warwick, Ruhr University Bochum, Cornell University,
Northwestern University, and Drexel University. Operations are conducted by COO,
IPAC, and UW.\r\n\r\nThis work has made use of data from the European Space Agency
(ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data
Processing and Analysis Consortium (DPAC; https://www.cosmos.esa.int/web/gaia/dpac/consortium).
Funding for the DPAC has been provided by national institutions, in particular,
the institutions participating in the Gaia Multilateral Agreement. This publication
makes use of data products from the Wide-field Infrared Survey Explorer, which is
a joint project of the University of California, Los Angeles, and the Jet Propulsion
Laboratory/California Institute of Technology, funded by the National Aeronautics
and Space Administration.\r\n\r\nThis research has made use of the VizieR catalog
access tool, CDS, Strasbourg, France https://vizier.cds.unistra.fr/. The original
description of the VizieR service was published in Ochsenbein et al. (2000).\r\n\r\nWe
are grateful to the staffs of Palomar and Keck Observatory for assistance with the
observations and data management.\r\n\r\nThe authors thank the anonymous referee
for very extensive and useful comments which improved the presentation of the paper
significantly. S.B. acknowledges the support from the Kishore Vaigyanik Protsahan
Yojana (KVPY) scheme of the Department of Science and Technology, Government of
India (a former fellowship program for undergraduate studies in basic science) during
his undergraduate studies at IISc. S.B. thanks the Summer Undergraduate Research
Fellowship (SURF) at Caltech and Shrinivas R. Kulkarni for hosting him as a summer
research student in 2022. S.B. acknowledges the financial support from the Wallace
L. W. Sargent Graduate Fellowship during the first year of his graduate studies
at Caltech. P.E.T. received funding from the European Research Council under the
European Union’s Horizon 2020 research and innovation program number 101002408.
S.X. is supported by NOIRLab, which is managed by the Association of Universities
for Research in Astronomy (AURA) under a cooperative agreement with the National
Science Foundation. J.A.G. is supported by the National Science Foundation Graduate
Research Fellowship Program under grant No. 2234657. This material is based upon
work supported by the National Aeronautics and Space Administration under grant
No. 80NSSC23K1068 issued through the Science Mission Directorate.\r\n\r\nWe have
used Python packages Numpy (Harris et al. 2020), SciPy (Virtanen et al. 2020), Matplotlib
(Hunter 2007), Pandas (The pandas development team 2020), Astropy (Astropy Collaboration
et al. 2013, 2018), and Astroquery (Ginsburg et al. 2019) at various stages of this
research."
article_number: '074202'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: 'Soumyadeep '
full_name: 'Bhattacharjee, Soumyadeep '
last_name: Bhattacharjee
- first_name: Zachary P.
full_name: Vanderbosch, Zachary P.
last_name: Vanderbosch
- first_name: Mark A.
full_name: Hollands, Mark A.
last_name: Hollands
- first_name: Pier-Emmanuel
full_name: Tremblay, Pier-Emmanuel
last_name: Tremblay
- first_name: Siyi
full_name: Xu, Siyi
last_name: Xu
- first_name: Joseph A.
full_name: Guidry, Joseph A.
last_name: Guidry
- first_name: J.J.
full_name: Hermes, J.J.
last_name: Hermes
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Antonio C.
full_name: Rodriguez, Antonio C.
last_name: Rodriguez
- first_name: Jan
full_name: van Roestel, Jan
last_name: van Roestel
- first_name: 'Kareem '
full_name: 'El-Badry, Kareem '
last_name: El-Badry
- first_name: Andrew J.
full_name: Drake, Andrew J.
last_name: Drake
- first_name: Benjamin R.
full_name: Roulston, Benjamin R.
last_name: Roulston
- first_name: Reed
full_name: Riddle, Reed
last_name: Riddle
- first_name: Ben
full_name: Rusholme, Ben
last_name: Rusholme
- first_name: Steven L.
full_name: Groom, Steven L.
last_name: Groom
- first_name: Roger
full_name: Smith, Roger
last_name: Smith
- first_name: Odette
full_name: Toloza, Odette
last_name: Toloza
citation:
ama: 'Bhattacharjee S, Vanderbosch ZP, Hollands MA, et al. A ZTF search for circumstellar
debris transits in White Dwarfs: Six new candidates, one with gas disk emission,
identified in a novel metric space. Publications of the Astronomical Society
of the Pacific. 2025;137(7). doi:10.1088/1538-3873/ade0ea'
apa: 'Bhattacharjee, S., Vanderbosch, Z. P., Hollands, M. A., Tremblay, P.-E., Xu,
S., Guidry, J. A., … Toloza, O. (2025). A ZTF search for circumstellar debris
transits in White Dwarfs: Six new candidates, one with gas disk emission, identified
in a novel metric space. Publications of the Astronomical Society of the Pacific.
IOP Publishing. https://doi.org/10.1088/1538-3873/ade0ea'
chicago: 'Bhattacharjee, Soumyadeep , Zachary P. Vanderbosch, Mark A. Hollands,
Pier-Emmanuel Tremblay, Siyi Xu, Joseph A. Guidry, J.J. Hermes, et al. “A ZTF
Search for Circumstellar Debris Transits in White Dwarfs: Six New Candidates,
One with Gas Disk Emission, Identified in a Novel Metric Space.” Publications
of the Astronomical Society of the Pacific. IOP Publishing, 2025. https://doi.org/10.1088/1538-3873/ade0ea.'
ieee: 'S. Bhattacharjee et al., “A ZTF search for circumstellar debris transits
in White Dwarfs: Six new candidates, one with gas disk emission, identified in
a novel metric space,” Publications of the Astronomical Society of the Pacific,
vol. 137, no. 7. IOP Publishing, 2025.'
ista: 'Bhattacharjee S, Vanderbosch ZP, Hollands MA, Tremblay P-E, Xu S, Guidry
JA, Hermes JJ, Caiazzo I, Rodriguez AC, van Roestel J, El-Badry K, Drake AJ, Roulston
BR, Riddle R, Rusholme B, Groom SL, Smith R, Toloza O. 2025. A ZTF search for
circumstellar debris transits in White Dwarfs: Six new candidates, one with gas
disk emission, identified in a novel metric space. Publications of the Astronomical
Society of the Pacific. 137(7), 074202.'
mla: 'Bhattacharjee, Soumyadeep, et al. “A ZTF Search for Circumstellar Debris Transits
in White Dwarfs: Six New Candidates, One with Gas Disk Emission, Identified in
a Novel Metric Space.” Publications of the Astronomical Society of the Pacific,
vol. 137, no. 7, 074202, IOP Publishing, 2025, doi:10.1088/1538-3873/ade0ea.'
short: S. Bhattacharjee, Z.P. Vanderbosch, M.A. Hollands, P.-E. Tremblay, S. Xu,
J.A. Guidry, J.J. Hermes, I. Caiazzo, A.C. Rodriguez, J. van Roestel, K. El-Badry,
A.J. Drake, B.R. Roulston, R. Riddle, B. Rusholme, S.L. Groom, R. Smith, O. Toloza,
Publications of the Astronomical Society of the Pacific 137 (2025).
date_created: 2026-02-16T15:10:51Z
date_published: 2025-07-09T00:00:00Z
date_updated: 2026-02-17T11:35:53Z
day: '09'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1088/1538-3873/ade0ea
external_id:
arxiv:
- '2502.05502'
file:
- access_level: open_access
checksum: 237eddc36e3823b3092fab6aa5bc8655
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T11:30:29Z
date_updated: 2026-02-17T11:30:29Z
file_id: '21289'
file_name: 2025_PASP_Bhattacharjee.pdf
file_size: 8900420
relation: main_file
success: 1
file_date_updated: 2026-02-17T11:30:29Z
has_accepted_license: '1'
intvolume: ' 137'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '07'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
issn:
- 1538-3873
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: 'A ZTF search for circumstellar debris transits in White Dwarfs: Six new candidates,
one with gas disk emission, identified in a novel metric space'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21243'
abstract:
- lang: eng
text: Widely deployed consensus protocols in the cloud are often leader-based and
optimized for low latency under synchronous network conditions. However, cloud
networks can experience disruptions such as network partitions, high-loss links,
and configuration errors. These disruptions interfere with the operation of leader-based
protocols, as their view change mechanisms interrupt the normal case replication
and cause the system to stall. We propose RACS, a novel randomized consensus protocol
that ensures robustness against adversarial network conditions. RACS achieves
optimal one-round trip latency under synchronous network conditions while remaining
resilient to adversarial network conditions. RACS follows a simple design inspired
by Raft, the most widely used consensus protocol in the cloud, and therefore enables
seamless integration with the existing cloud software stack. Experiments with
a prototype running on Amazon EC2 show that RACS achieves 28k cmd/sec throughput,
ninefold higher than Raft under adversarial cloud network conditions. Under synchronous
network conditions, RACS matches the performance of Multi-Paxos and Raft, achieving
a throughput of 200k cmd/sec with a median latency of 300ms, confirming that RACS
introduces no unnecessary overhead. Finally, SADL-RACS, a throughput-optimized
version of RACS, achieves a throughput of 500k cmd/sec, delivering 150 percent
higher throughput than Raft.
article_processing_charge: No
arxiv: 1
author:
- first_name: Pasindu
full_name: Tennage, Pasindu
last_name: Tennage
- first_name: Antoine
full_name: Desjardins, Antoine
id: 06d0c166-aec1-11ee-a7c0-b96e840a602b
last_name: Desjardins
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
orcid: 0000-0002-8827-3382
citation:
ama: 'Tennage P, Desjardins A, Kokoris Kogias E. RACS-SADL: Robust and understandable
randomized consensus in the cloud. In: 2025 IEEE 18th International Conference
on Cloud Computing. IEEE; 2025. doi:10.1109/cloud67622.2025.00044'
apa: 'Tennage, P., Desjardins, A., & Kokoris Kogias, E. (2025). RACS-SADL: Robust
and understandable randomized consensus in the cloud. In 2025 IEEE 18th International
Conference on Cloud Computing. Helsinki, Finland: IEEE. https://doi.org/10.1109/cloud67622.2025.00044'
chicago: 'Tennage, Pasindu, Antoine Desjardins, and Eleftherios Kokoris Kogias.
“RACS-SADL: Robust and Understandable Randomized Consensus in the Cloud.” In 2025
IEEE 18th International Conference on Cloud Computing. IEEE, 2025. https://doi.org/10.1109/cloud67622.2025.00044.'
ieee: 'P. Tennage, A. Desjardins, and E. Kokoris Kogias, “RACS-SADL: Robust and
understandable randomized consensus in the cloud,” in 2025 IEEE 18th International
Conference on Cloud Computing, Helsinki, Finland, 2025.'
ista: 'Tennage P, Desjardins A, Kokoris Kogias E. 2025. RACS-SADL: Robust and understandable
randomized consensus in the cloud. 2025 IEEE 18th International Conference on
Cloud Computing. CLOUD: Conference on Cloud Computing.'
mla: 'Tennage, Pasindu, et al. “RACS-SADL: Robust and Understandable Randomized
Consensus in the Cloud.” 2025 IEEE 18th International Conference on Cloud Computing,
IEEE, 2025, doi:10.1109/cloud67622.2025.00044.'
short: P. Tennage, A. Desjardins, E. Kokoris Kogias, in:, 2025 IEEE 18th International
Conference on Cloud Computing, IEEE, 2025.
conference:
end_date: 2025-07-12
location: Helsinki, Finland
name: 'CLOUD: Conference on Cloud Computing'
start_date: 2025-07-07
corr_author: '1'
date_created: 2026-02-16T15:21:27Z
date_published: 2025-07-30T00:00:00Z
date_updated: 2026-05-05T11:52:57Z
day: '30'
department:
- _id: ElKo
doi: 10.1109/cloud67622.2025.00044
external_id:
arxiv:
- '2404.04183'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.04183
month: '07'
oa: 1
oa_version: Preprint
publication: 2025 IEEE 18th International Conference on Cloud Computing
publication_identifier:
eisbn:
- '9798331555573'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'RACS-SADL: Robust and understandable randomized consensus in the cloud'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21245'
abstract:
- lang: eng
text: Flickering light is a new promising, fully non-invasive brain stimulation
technique that utilizes intermittent sensory stimulation to induce brainwave synchronization
(entrainment). While the effects of 40 Hz externally induced neural entrainment
have been extensively described, little is known about 60 Hz entrainment in humans.
This study presents preliminary observations on the neural and somatic response
to flickering 60 Hz light in healthy volunteers over a 3-week period. Fourteen
volunteers were randomized to receive either 60 Hz flickering white light or constant
light as sham (30-min sessions, 3 weeks, 5 days/week on weekdays). Neural entrainment
was assessed with EEG on days 1, 5 and 19. Salivary cortisol and C-reactive protein
(CRP) levels, measured with ELISA, assessed the somatic response to stimulation.
Side effects and well-being were monitored via questionnaires. EEG recordings
showed neural entrainment and synchrony in response to 60 Hz flickering light
across multiple cortical regions, including occipital, central, temporal, and
frontal areas. The entrainment power and synchronization between different cortical
regions declined significantly by day 19 compared to day 1, indicating possible
neural habituation. Cortisol and CRP salivary levels were unchanged, and minor
side effects were reported with equal frequency in the active and sham groups.
Our findings show that 60 Hz flickering light can induce significant neural entrainment
and synchrony in healthy adults and is well tolerated. The decline in entrainment
strength and neural synchrony observed with repeated 60 Hz stimulations suggests
plastic changes in the cortex. To the best of our knowledge, this is the first
study to characterize neural and somatic responses to repeated 60 Hz flickering
visual stimuli. Given the well-known connection between 60 Hz brain oscillations
and cognition, neuroplasticity, and their role in neuropsychiatric disorders,
additional research in both preclinical and clinical settings is warranted.
acknowledgement: This study was funded by Syntropic Medical and supported by an Austria
Wirtschaftsservice (AWS) grant (grant number P2414247 to Syntropic Medical). Syntropic
Medical employees were involved in study design, data collection and analysis, decision
to publish, and preparation of the manuscript. AWS had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.
article_number: e0332310
article_processing_charge: Yes
article_type: original
author:
- first_name: MohammadAmin
full_name: Alamalhoda, MohammadAmin
last_name: Alamalhoda
- first_name: Friederike
full_name: Leesch, Friederike
last_name: Leesch
- first_name: Francesca
full_name: Giovanetti, Francesca
last_name: Giovanetti
- first_name: Eoghan
full_name: Dunne, Eoghan
last_name: Dunne
- first_name: Giuseppina
full_name: Pilloni, Giuseppina
last_name: Pilloni
- first_name: Mark
full_name: Caffrey, Mark
last_name: Caffrey
- first_name: Jack
full_name: O’Keeffe, Jack
last_name: O’Keeffe
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Maria Teresa
full_name: Ferretti, Maria Teresa
last_name: Ferretti
citation:
ama: Alamalhoda M, Leesch F, Giovanetti F, et al. Exploring neural entrainment and
synchrony in response to repeated 60 Hz flickering white light in healthy volunteers.
PLOS One. 2025;20(10). doi:10.1371/journal.pone.0332310
apa: Alamalhoda, M., Leesch, F., Giovanetti, F., Dunne, E., Pilloni, G., Caffrey,
M., … Ferretti, M. T. (2025). Exploring neural entrainment and synchrony in response
to repeated 60 Hz flickering white light in healthy volunteers. PLOS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0332310
chicago: Alamalhoda, MohammadAmin, Friederike Leesch, Francesca Giovanetti, Eoghan
Dunne, Giuseppina Pilloni, Mark Caffrey, Jack O’Keeffe, Alessandro Venturino,
and Maria Teresa Ferretti. “Exploring Neural Entrainment and Synchrony in Response
to Repeated 60 Hz Flickering White Light in Healthy Volunteers.” PLOS One.
Public Library of Science, 2025. https://doi.org/10.1371/journal.pone.0332310.
ieee: M. Alamalhoda et al., “Exploring neural entrainment and synchrony in
response to repeated 60 Hz flickering white light in healthy volunteers,” PLOS
One, vol. 20, no. 10. Public Library of Science, 2025.
ista: Alamalhoda M, Leesch F, Giovanetti F, Dunne E, Pilloni G, Caffrey M, O’Keeffe
J, Venturino A, Ferretti MT. 2025. Exploring neural entrainment and synchrony
in response to repeated 60 Hz flickering white light in healthy volunteers. PLOS
One. 20(10), e0332310.
mla: Alamalhoda, MohammadAmin, et al. “Exploring Neural Entrainment and Synchrony
in Response to Repeated 60 Hz Flickering White Light in Healthy Volunteers.” PLOS
One, vol. 20, no. 10, e0332310, Public Library of Science, 2025, doi:10.1371/journal.pone.0332310.
short: M. Alamalhoda, F. Leesch, F. Giovanetti, E. Dunne, G. Pilloni, M. Caffrey,
J. O’Keeffe, A. Venturino, M.T. Ferretti, PLOS One 20 (2025).
date_created: 2026-02-16T15:29:26Z
date_published: 2025-10-07T00:00:00Z
date_updated: 2026-02-17T12:19:15Z
day: '07'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1371/journal.pone.0332310
external_id:
pmid:
- '41056352 '
file:
- access_level: open_access
checksum: 22a4e92a733152633c4553f107f66765
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T12:16:18Z
date_updated: 2026-02-17T12:16:18Z
file_id: '21301'
file_name: 2025_PlosOne_Alamalhoda.pdf
file_size: 1388424
relation: main_file
success: 1
file_date_updated: 2026-02-17T12:16:18Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS One
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/AminAlam/HVS
status: public
title: Exploring neural entrainment and synchrony in response to repeated 60 Hz flickering
white light in healthy volunteers
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: 20
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21246'
abstract:
- lang: eng
text: Stellar astrophysics relies on diverse observational modalities—primarily
photometric light curves and spectroscopic data—from which fundamental stellar
properties are inferred. While machine learning (ML) has advanced analysis within
individual modalities, the complementary information encoded across modalities
remains largely underexploited. We present the dual embedding for stellar astronomy
(DESA) model, a novel multimodal foundation model that integrates light curves
and spectra to learn a unified, physically meaningful latent space for stars.
DESA first trains separate modality-specific encoders using a hybrid supervised/self-supervised
scheme, and then aligns them through DualFormer, a transformer-based cross-modal
integration module tailored for astrophysical data. DualFormer combines cross-
and self-attention, a novel dual-projection alignment loss, and a projection-space
eigendecomposition that yields physically structured embeddings. We demonstrate
that DESA significantly outperforms leading unimodal and self-supervised baselines
across a range of tasks. In zero- and few-shot settings, DESA’s learned representations
recover stellar color–magnitude and Hertzsprung–Russell diagrams with high fidelity
(R2 = 0.92 for photometric regressions). In full fine-tuning, DESA achieves state-of-the-art
accuracy for binary star detection (AUC = 0.99, AP = 1.00) and stellar age prediction
(RMSE = 0.94 Gyr). As a compelling case, DESA naturally separates synchronized
binaries from young stars—two populations with nearly identical light curves—purely
from their embedded positions in UMAP space, without requiring external kinematic
or luminosity information. DESA thus offers a powerful new framework for multimodal,
data-driven stellar population analysis, enabling both accurate prediction and
novel discovery.
acknowledgement: This research was partially supported by the Israeli Science Foundation
grant 1834/24.
article_number: '110'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Ilay
full_name: Kamai, Ilay
last_name: Kamai
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Hagai B.
full_name: Perets, Hagai B.
last_name: Perets
citation:
ama: Kamai I, Bronstein AM, Perets HB. Machine Learning inference of stellar properties
using integrated photometric and spectroscopic data. The Astrophysical Journal.
2025;994. doi:10.3847/1538-4357/ae0cbc
apa: Kamai, I., Bronstein, A. M., & Perets, H. B. (2025). Machine Learning inference
of stellar properties using integrated photometric and spectroscopic data. The
Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ae0cbc
chicago: Kamai, Ilay, Alex M. Bronstein, and Hagai B. Perets. “Machine Learning
Inference of Stellar Properties Using Integrated Photometric and Spectroscopic
Data.” The Astrophysical Journal. IOP Publishing, 2025. https://doi.org/10.3847/1538-4357/ae0cbc.
ieee: I. Kamai, A. M. Bronstein, and H. B. Perets, “Machine Learning inference of
stellar properties using integrated photometric and spectroscopic data,” The
Astrophysical Journal, vol. 994. IOP Publishing, 2025.
ista: Kamai I, Bronstein AM, Perets HB. 2025. Machine Learning inference of stellar
properties using integrated photometric and spectroscopic data. The Astrophysical
Journal. 994, 110.
mla: Kamai, Ilay, et al. “Machine Learning Inference of Stellar Properties Using
Integrated Photometric and Spectroscopic Data.” The Astrophysical Journal,
vol. 994, 110, IOP Publishing, 2025, doi:10.3847/1538-4357/ae0cbc.
short: I. Kamai, A.M. Bronstein, H.B. Perets, The Astrophysical Journal 994 (2025).
date_created: 2026-02-16T15:35:29Z
date_published: 2025-11-19T00:00:00Z
date_updated: 2026-02-17T12:33:19Z
day: '19'
ddc:
- '520'
- '000'
department:
- _id: AlBr
doi: 10.3847/1538-4357/ae0cbc
external_id:
arxiv:
- '2507.10666'
file:
- access_level: open_access
checksum: 255ffd6d664e6c2d1cffbaced650bd10
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T12:32:18Z
date_updated: 2026-02-17T12:32:18Z
file_id: '21302'
file_name: 2025_AstrophysicalJournal_Kamai.pdf
file_size: 16415089
relation: main_file
success: 1
file_date_updated: 2026-02-17T12:32:18Z
has_accepted_license: '1'
intvolume: ' 994'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Machine Learning inference of stellar properties using integrated photometric
and spectroscopic data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 994
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21247'
abstract:
- lang: eng
text: Seasonal snowmelt in High Mountain Asia is an important source of river discharge.
Therefore, observation of the spatiotemporal variations in snow cover at catchment
scales using high-resolution satellites is essential for understanding changes
in water supply from headwater catchments. In this study, we adapt an algorithm
to automatically detect the snowline altitude (SLA) using the Google Earth Engine
platform with available high-resolution multispectral satellite archives that
can be readily applied for areas of interest. Here, we applied and evaluated the
tool to five glacierized watersheds across the Himalayas to quantify the changes
in seasonal and annual snow cover over the past 21 years and analyze climate reanalysis
data to assess the meteorological factors influencing the SLA. Our findings revealed
substantial variations in the SLA among sites in terms of seasonal patterns, decadal
trends, and meteorological controls. We identify positive trends in SLA in Hidden
Valley (+11.9 m yr−1), Langtang (+14.4 m yr−1), and Rolwaling (+8.2 m yr−1) in
the Nepalese Himalayas but a negative trend in Satopanth (−15.6 m yr−1) in the
western Indian Himalayas and no significant trend in Parlung in southeastern Tibet.
We suggest that the increase in SLA in Nepal was caused by warmer temperatures
during the monsoon season, whereas the decrease in SLA in India was driven by
increased winter snowfall and reduced monsoon snowmelt. By integrating the outcomes
of these analyses, we found that long-term changes in SLA are primarily driven
by shifts in the local climate, whereas seasonal variability may be influenced
by geographic features in conjunction with climate.
acknowledgement: We thank Maud Bernat for helping with the modification of the automatic
detection code and Michael McCarthy for preparing snowline data derived from the
MODIS satellite. This research was supported by the JSPS–SNSF (Japan Society for
the Promotion of Science–Swiss National Science Foundation) bilateral program project
(HOPE, High-elevation precipitation in High Mountain Asia; JPJSJRP 20191503, grant
no. 183633) and JSPS KAKENHI (grant nos. 23K13417 and 23H01509).
article_processing_charge: No
article_type: original
author:
- first_name: Orie
full_name: Sasaki, Orie
last_name: Sasaki
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
- first_name: Akiko
full_name: Sakai, Akiko
last_name: Sakai
- first_name: Koji
full_name: Fujita, Koji
last_name: Fujita
citation:
ama: Sasaki O, Miles ES, Pellicciotti F, Sakai A, Fujita K. Contrasting patterns
of change in snowline altitude across five Himalayan catchments. The Cryosphere.
2025;19(11):5283-5298. doi:10.5194/tc-19-5283-2025
apa: Sasaki, O., Miles, E. S., Pellicciotti, F., Sakai, A., & Fujita, K. (2025).
Contrasting patterns of change in snowline altitude across five Himalayan catchments.
The Cryosphere. Copernicus Publications. https://doi.org/10.5194/tc-19-5283-2025
chicago: Sasaki, Orie, Evan S. Miles, Francesca Pellicciotti, Akiko Sakai, and Koji
Fujita. “Contrasting Patterns of Change in Snowline Altitude across Five Himalayan
Catchments.” The Cryosphere. Copernicus Publications, 2025. https://doi.org/10.5194/tc-19-5283-2025.
ieee: O. Sasaki, E. S. Miles, F. Pellicciotti, A. Sakai, and K. Fujita, “Contrasting
patterns of change in snowline altitude across five Himalayan catchments,” The
Cryosphere, vol. 19, no. 11. Copernicus Publications, pp. 5283–5298, 2025.
ista: Sasaki O, Miles ES, Pellicciotti F, Sakai A, Fujita K. 2025. Contrasting patterns
of change in snowline altitude across five Himalayan catchments. The Cryosphere.
19(11), 5283–5298.
mla: Sasaki, Orie, et al. “Contrasting Patterns of Change in Snowline Altitude across
Five Himalayan Catchments.” The Cryosphere, vol. 19, no. 11, Copernicus
Publications, 2025, pp. 5283–98, doi:10.5194/tc-19-5283-2025.
short: O. Sasaki, E.S. Miles, F. Pellicciotti, A. Sakai, K. Fujita, The Cryosphere
19 (2025) 5283–5298.
date_created: 2026-02-16T15:36:51Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-02-17T12:49:00Z
day: '01'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.5194/tc-19-5283-2025
file:
- access_level: open_access
checksum: 2bb8ada7536bb69b39448f13098f8cea
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T12:35:44Z
date_updated: 2026-02-17T12:35:44Z
file_id: '21303'
file_name: 2025_Cryosphere_Sasaki.pdf
file_size: 6617241
relation: main_file
success: 1
file_date_updated: 2026-02-17T12:35:44Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 5283-5298
publication: The Cryosphere
publication_identifier:
eissn:
- 1994-0424
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
status: public
title: Contrasting patterns of change in snowline altitude across five Himalayan catchments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21248'
abstract:
- lang: eng
text: Camera-type eyes in vertebrates and cephalopods are striking examples of parallel
evolution of a complex structure. While comparisons have focused on these two
groups, camera-type eyes with likely high functionality are also found in other
invertebrate phyla with simpler brains. Employing single-cell RNA sequencing,
we identify neurogenic cells in the adult eyes and brain of the marine annelid
worm Platynereis dumerilii. Distinct neural stem cells in the camera-type adult
eyes, located at the edge of the cup-shaped retina, and adjacent to the glass
body/lens, produce radial lines of cells, reminiscent of stem cells in ciliary
marginal zones of vertebrate eyes exhibiting life-long growth. Normal proliferation
in the eye depends on ambient light, a phenomenon that depends on the integrity
of the photoreceptor gene c-opsin1, which is present in emerging rhabdomeric photoreceptors,
and impacts on their differentiation. During reproductive maturation, proliferation
in the eye as well as the entire brain sharply declines, while cells upregulate
molecular characteristics of mammalian adult neural stem cell quiescence. Our
data provide insights into the development and modulation of annelid head and
brain cells, revealing similarities and differences to vertebrate eye development,
neurogenesis and brain plasticity.
acknowledgement: 'We are grateful to Andrij Belokurov, Margaryta Borysova and Netsanet
Getachew for routine worm cultures and genotyping support, Lena Stumbauer for practical
help, as well as all members of the Tessmar-Raible and Raible labs for constructive
discussions. This work was supported by, Helmholtz Society, distinguished professorship
by the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (K.T.-R.),
H2020 European Research Council, ERC Grant Agreement #819952 (K.T.-R.), Austrian
Science Funds (FWF), SFB F78 (F.R., K.T-R; https://doi.org/10.55776/F78), the Human
Frontier Science Program (HFSP), #RGP021/2024, https://doi.org/10.52044/HFSP.RGP0212024.pc.gr.194174
(KT-R), University of Vienna Research Platform SinCeReSt (F.R.), For open access
purposes, K.T.-R. has applied a CC BY public copyright license to any author accepted
manuscript version arising from this submission. We acknowledge support by the Open
Access publication fund of Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-
und Meeresforschung. None of the funding bodies was involved in the design of the
study, the collection, analysis, and interpretation of data or in writing the manuscript.
Open Access funding enabled and organized by Projekt DEAL.'
article_number: '9861'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nadja
full_name: Milivojev, Nadja
last_name: Milivojev
- first_name: Federico
full_name: Scaramuzza, Federico
last_name: Scaramuzza
- first_name: Pedro Ozório
full_name: Brum, Pedro Ozório
last_name: Brum
- first_name: Camila L
full_name: Velastegui Gamboa, Camila L
id: 625aea67-91c1-11f0-aad8-f71452b4174d
last_name: Velastegui Gamboa
- first_name: Gabriele
full_name: Andreatta, Gabriele
last_name: Andreatta
- first_name: Florian
full_name: Raible, Florian
last_name: Raible
- first_name: Kristin
full_name: Tessmar-Raible, Kristin
last_name: Tessmar-Raible
citation:
ama: Milivojev N, Scaramuzza F, Brum PO, et al. Light-modulated stem cells in the
camera-type eye of an annelid model for adult brain plasticity. Nature Communications.
2025;16. doi:10.1038/s41467-025-65631-0
apa: Milivojev, N., Scaramuzza, F., Brum, P. O., Velastegui Gamboa, C. L., Andreatta,
G., Raible, F., & Tessmar-Raible, K. (2025). Light-modulated stem cells in
the camera-type eye of an annelid model for adult brain plasticity. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65631-0
chicago: Milivojev, Nadja, Federico Scaramuzza, Pedro Ozório Brum, Camila L Velastegui
Gamboa, Gabriele Andreatta, Florian Raible, and Kristin Tessmar-Raible. “Light-Modulated
Stem Cells in the Camera-Type Eye of an Annelid Model for Adult Brain Plasticity.”
Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65631-0.
ieee: N. Milivojev et al., “Light-modulated stem cells in the camera-type
eye of an annelid model for adult brain plasticity,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Milivojev N, Scaramuzza F, Brum PO, Velastegui Gamboa CL, Andreatta G, Raible
F, Tessmar-Raible K. 2025. Light-modulated stem cells in the camera-type eye of
an annelid model for adult brain plasticity. Nature Communications. 16, 9861.
mla: Milivojev, Nadja, et al. “Light-Modulated Stem Cells in the Camera-Type Eye
of an Annelid Model for Adult Brain Plasticity.” Nature Communications,
vol. 16, 9861, Springer Nature, 2025, doi:10.1038/s41467-025-65631-0.
short: N. Milivojev, F. Scaramuzza, P.O. Brum, C.L. Velastegui Gamboa, G. Andreatta,
F. Raible, K. Tessmar-Raible, Nature Communications 16 (2025).
date_created: 2026-02-16T15:38:11Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-06-18T18:30:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1038/s41467-025-65631-0
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-025-65631-0
month: '12'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-modulated stem cells in the camera-type eye of an annelid model for adult
brain plasticity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21250'
abstract:
- lang: eng
text: We investigate the step complexity of the Leader Election problem (and implementing
the corresponding test-and-set object) in asynchronous shared memory, where processes
communicate through registers supporting atomic read and write and must coordinate
so that a single process becomes the leader. Determining tight step complexity
bounds for solving this problem is one of the key open problems in the theory
of shared memory distributed computing. The best known algorithm is a randomized
tournament-tree, which has worst-case expected step complexity O(log N) for N
processes. There are provably no deterministic wait-free algorithms, and only
restricted lower bounds are known for obstruction-free and randomized wait-free
algorithms. We introduce a new lower bound that establishes an Ω((log N)/(log
log N + log Q)) step complexity for any obstruction-free Leader Election algorithm,
where N is the number of processes, and 2 ≤ Q ≤ N is a bound on the value contention,
which we define as the maximum number of different values that processes can be
simultaneously poised to write to the same register in any execution of the algorithm.
Our result is strictly stronger than previous bounds based on write contention.
In particular, it implies new lower bounds on step complexity that depend on register
size.
acknowledgement: The work of Dan Alistarh is supported by grants from ERC, Austrian
FWF, and the Google and NVIDIA corporations. Faith Ellen was supported in part by
the Natural Science and Engineering Research Council of Canada (NSERC) grant RGPIN-2020-04178.
alternative_title:
- LIPIcs
article_processing_charge: Yes
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
citation:
ama: 'Alistarh D-A, Ellen F, Fedorov A. An almost-logarithmic lower bound for leader
election with bounded value contention. In: 39th International Symposium on
Distributed Computing. Vol 356. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2025:3:1-3:16. doi:10.4230/LIPIcs.DISC.2025.3'
apa: 'Alistarh, D.-A., Ellen, F., & Fedorov, A. (2025). An almost-logarithmic
lower bound for leader election with bounded value contention. In 39th International
Symposium on Distributed Computing (Vol. 356, p. 3:1-3:16). Berlin, Germany:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2025.3'
chicago: Alistarh, Dan-Adrian, Faith Ellen, and Alexander Fedorov. “An Almost-Logarithmic
Lower Bound for Leader Election with Bounded Value Contention.” In 39th International
Symposium on Distributed Computing, 356:3:1-3:16. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2025. https://doi.org/10.4230/LIPIcs.DISC.2025.3.
ieee: D.-A. Alistarh, F. Ellen, and A. Fedorov, “An almost-logarithmic lower bound
for leader election with bounded value contention,” in 39th International Symposium
on Distributed Computing, Berlin, Germany, 2025, vol. 356, p. 3:1-3:16.
ista: 'Alistarh D-A, Ellen F, Fedorov A. 2025. An almost-logarithmic lower bound
for leader election with bounded value contention. 39th International Symposium
on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol.
356, 3:1-3:16.'
mla: Alistarh, Dan-Adrian, et al. “An Almost-Logarithmic Lower Bound for Leader
Election with Bounded Value Contention.” 39th International Symposium on Distributed
Computing, vol. 356, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025,
p. 3:1-3:16, doi:10.4230/LIPIcs.DISC.2025.3.
short: D.-A. Alistarh, F. Ellen, A. Fedorov, in:, 39th International Symposium on
Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025,
p. 3:1-3:16.
conference:
end_date: 2025-10-31
location: Berlin, Germany
name: 'DISC: Symposium on Distributed Computing'
start_date: 2025-10-27
corr_author: '1'
date_created: 2026-02-16T15:41:15Z
date_published: 2025-10-22T00:00:00Z
date_updated: 2026-02-18T06:49:38Z
day: '22'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.4230/LIPIcs.DISC.2025.3
file:
- access_level: open_access
checksum: 3825a0e6e6a05503e842a59f95528bd9
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T06:46:02Z
date_updated: 2026-02-18T06:46:02Z
file_id: '21310'
file_name: 2025_LIPIcs_Alistarh.pdf
file_size: 1492189
relation: main_file
success: 1
file_date_updated: 2026-02-18T06:46:02Z
has_accepted_license: '1'
intvolume: ' 356'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3:1-3:16
publication: 39th International Symposium on Distributed Computing
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: An almost-logarithmic lower bound for leader election with bounded value contention
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21251'
abstract:
- lang: eng
text: Cellular membranes differ across the tree of life. In most bacteria and eukaryotes,
single-headed lipids self-assemble into flexible bilayer membranes. By contrast,
thermophilic archaea tend to possess bilayer lipids together with double-headed,
monolayer spanning bolalipids, which are thought to enable cells to survive in
harsh environments. Here, using a minimal computational model for bolalipid membranes,
we explore the trade-offs at play when forming membranes. We find that flexible
bolalipids form membranes that resemble bilayer membranes because they are able
to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble
the bolalipids with cyclic groups found in thermophilic archaea, take on a straight
conformation and form membranes that are stiff and prone to pore formation when
they undergo changes in shape. Strikingly, however, the inclusion of small amounts
of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid
membranes that are both stable and flexible, resolving this trade-off. Our study
suggests a mechanism by which archaea can tune the material properties of their
membranes as and when required to enable them to survive in harsh environments
and to undergo essential membrane remodelling events like cell division.
acknowledgement: MA, BB, and AŠ acknowledge funding by the Volkswagen Foundation Grant
Az 96727. FF acknowledges financial support by the NOMIS foundation. AŠ acknowledges
funding by ERC Starting Grant 'NEPA' 802960. We thank Claudia Flandoli for her help
with illustrations.
article_number: '105432'
article_processing_charge: Yes
article_type: original
author:
- first_name: Miguel
full_name: Santana de Freitas Amaral, Miguel
id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501
last_name: Santana de Freitas Amaral
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Balancing stability
and flexibility when reshaping archaeal membranes. eLife. 2025;14. doi:10.7554/elife.105432
apa: Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić,
A. (2025). Balancing stability and flexibility when reshaping archaeal membranes.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.105432
chicago: Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum,
and Anđela Šarić. “Balancing Stability and Flexibility When Reshaping Archaeal
Membranes.” ELife. eLife Sciences Publications, 2025. https://doi.org/10.7554/elife.105432.
ieee: M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić,
“Balancing stability and flexibility when reshaping archaeal membranes,” eLife,
vol. 14. eLife Sciences Publications, 2025.
ista: Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. 2025. Balancing
stability and flexibility when reshaping archaeal membranes. eLife. 14, 105432.
mla: Santana de Freitas Amaral, Miguel, et al. “Balancing Stability and Flexibility
When Reshaping Archaeal Membranes.” ELife, vol. 14, 105432, eLife Sciences
Publications, 2025, doi:10.7554/elife.105432.
short: M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, ELife
14 (2025).
corr_author: '1'
date_created: 2026-02-16T15:43:57Z
date_published: 2025-10-07T00:00:00Z
date_updated: 2026-02-23T11:49:05Z
day: '07'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.7554/elife.105432
ec_funded: 1
external_id:
pmid:
- '41056191 '
file:
- access_level: open_access
checksum: 4116cd5143558ded995fb9ff5fcbc7e0
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T13:02:02Z
date_updated: 2026-02-17T13:02:02Z
file_id: '21305'
file_name: 2025_elife_Amaral.pdf
file_size: 10668225
relation: main_file
success: 1
file_date_updated: 2026-02-17T13:02:02Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
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: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '21304'
relation: software
status: public
status: public
title: Balancing stability and flexibility when reshaping archaeal membranes
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: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21252'
abstract:
- lang: eng
text: "Context. Recent observational results from asteroseismic studies show that
an important fraction of solar-like stars do not present detectable stochastically
excited acoustic oscillations. This non-detectability seems to correlate with
a high rotation rate in the convective envelope and a high surface magnetic activity.
At the same time, the properties of stellar convection are affected by rotation
and magnetism.\r\nAims. We investigate the role of rotation in the excitation
of acoustic modes in the convective envelope of solar-like stars, to evaluate
its impact on the energy injected in the oscillations.\r\nMethods. We derived
theoretical prescriptions for the excitation of acoustic waves in the convective
envelope of rotating solar-like stars. We adopted the rotating mixing-length Theory
to model the influence of rotation on convection. We used the MESA stellar evolution
code and the GYRE stellar oscillation code to estimate the power injected in the
oscillations from our theoretical prescriptions.\r\nResults. We demonstrate that
the power injected in the acoustic modes is insensitive to rotation if a Gaussian
time-correlation function is assumed, while it can decrease by up to 60% for a
Lorentzian time-correlation function, for a 20 Ω⊙ rotation rate. We show that
the modification of the excitation rate by rotation depends not only on the rotation
rate but also on the radial and angular orders of the considered oscillation mode.
This result can allow for better constraints on the properties of stellar convection
by studying observationally acoustic mode excitation.\r\nConclusions. These results
demonstrate how important it is to take into account the modification of stellar
convection by rotation when evaluating the amplitude of the stellar oscillations
it stochastically excites. They open the path for understanding the large variety
of observed acoustic-mode amplitudes at the surface of solar-like stars as a function
of surface rotation rates."
acknowledgement: 'The authors thank the referee for detailed comments that allow them
to improve their work. The authors thank Jordan Philidet and Kevin Belkacem for
fruitful discussions. L.B. and Stéphane M. acknowledge support from the European
Research Council (ERC) under the Horizon Europe program (Synergy Grant agreement
101071505: 4D-STAR), from the CNES SOHO-GOLF and PLATO grants at CEA-DAp, and from
PNPS (CNRS/INSU). While partially funded by the European Union, views and opinions
expressed are however those of the author only and do not necessarily reflect those
of the European Union or the European Research Council. Neither the European Union
nor the granting authority can be held responsible for them. Savita M. acknowledges
support from the Spanish Ministry of Science and Innovation with the grant no. PID2019-107061GB-C66
and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023
(CEX2019-000920-S).'
article_number: A25
article_processing_charge: Yes
article_type: original
author:
- first_name: L.
full_name: Bessila, L.
last_name: Bessila
- first_name: A.
full_name: Deckx van Ruys, A.
last_name: Deckx van Ruys
- first_name: V.
full_name: Buriasco, V.
last_name: Buriasco
- first_name: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: R. A.
full_name: García, R. A.
last_name: García
- first_name: S.
full_name: Mathur, S.
last_name: Mathur
citation:
ama: Bessila L, Deckx van Ruys A, Buriasco V, et al. The impact of rotation on the
stochastic excitation of stellar acoustic modes in solar-like pulsators. Astronomy
& Astrophysics. 2025;700. doi:10.1051/0004-6361/202452093
apa: Bessila, L., Deckx van Ruys, A., Buriasco, V., Mathis, S., Bugnet, L. A., García,
R. A., & Mathur, S. (2025). The impact of rotation on the stochastic excitation
of stellar acoustic modes in solar-like pulsators. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/202452093
chicago: Bessila, L., A. Deckx van Ruys, V. Buriasco, S. Mathis, Lisa Annabelle
Bugnet, R. A. García, and S. Mathur. “The Impact of Rotation on the Stochastic
Excitation of Stellar Acoustic Modes in Solar-like Pulsators.” Astronomy &
Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202452093.
ieee: L. Bessila et al., “The impact of rotation on the stochastic excitation
of stellar acoustic modes in solar-like pulsators,” Astronomy & Astrophysics,
vol. 700. EDP Sciences, 2025.
ista: Bessila L, Deckx van Ruys A, Buriasco V, Mathis S, Bugnet LA, García RA, Mathur
S. 2025. The impact of rotation on the stochastic excitation of stellar acoustic
modes in solar-like pulsators. Astronomy & Astrophysics. 700, A25.
mla: Bessila, L., et al. “The Impact of Rotation on the Stochastic Excitation of
Stellar Acoustic Modes in Solar-like Pulsators.” Astronomy & Astrophysics,
vol. 700, A25, EDP Sciences, 2025, doi:10.1051/0004-6361/202452093.
short: L. Bessila, A. Deckx van Ruys, V. Buriasco, S. Mathis, L.A. Bugnet, R.A.
García, S. Mathur, Astronomy & Astrophysics 700 (2025).
date_created: 2026-02-16T15:46:59Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2026-02-17T13:10:18Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202452093
file:
- access_level: open_access
checksum: b8a0927307c1d82025bcb5af47b20b26
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T13:07:45Z
date_updated: 2026-02-17T13:07:45Z
file_id: '21306'
file_name: 2025_AstronomyAstrophysics_Bessila.pdf
file_size: 7161755
relation: main_file
success: 1
file_date_updated: 2026-02-17T13:07:45Z
has_accepted_license: '1'
intvolume: ' 700'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
status: public
title: The impact of rotation on the stochastic excitation of stellar acoustic modes
in solar-like pulsators
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: 700
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21253'
abstract:
- lang: eng
text: We solve a problem of Dujmović and Wood (2007) by showing that a complete
convex geometric graph on n vertices cannot be decomposed into fewer than n -
1 star-forests, each consisting of noncrossing edges. This bound is clearly tight.
We also discuss similar questions for abstract graphs.
acknowledgement: A preliminary version of this note has been published in the proceedings
of the 31st International Symposium on Graph Drawing and Network Visualization,
Palermo, 2023. The authors would like to thank the anonymous referees for their
valuable comments.
article_number: '102186'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: János
full_name: Pach, János
last_name: Pach
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
- first_name: Patrick
full_name: Schnider, Patrick
last_name: Schnider
citation:
ama: Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests.
Computational Geometry. 2025;129. doi:10.1016/j.comgeo.2025.102186
apa: Pach, J., Saghafian, M., & Schnider, P. (2025). Decomposition of geometric
graphs into star-forests. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2025.102186
chicago: Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of
Geometric Graphs into Star-Forests.” Computational Geometry. Elsevier,
2025. https://doi.org/10.1016/j.comgeo.2025.102186.
ieee: J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs
into star-forests,” Computational Geometry, vol. 129. Elsevier, 2025.
ista: Pach J, Saghafian M, Schnider P. 2025. Decomposition of geometric graphs into
star-forests. Computational Geometry. 129, 102186.
mla: Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.”
Computational Geometry, vol. 129, 102186, Elsevier, 2025, doi:10.1016/j.comgeo.2025.102186.
short: J. Pach, M. Saghafian, P. Schnider, Computational Geometry 129 (2025).
corr_author: '1'
date_created: 2026-02-16T15:48:42Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-04-16T09:12:36Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2025.102186
external_id:
arxiv:
- '2306.13201'
intvolume: ' 129'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.13201
month: '12'
oa: 1
oa_version: Preprint
publication: Computational Geometry
publication_identifier:
issn:
- 0925-7721
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '15012'
relation: earlier_version
status: public
status: public
title: Decomposition of geometric graphs into star-forests
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2025'
...
---
OA_type: closed access
_id: '21255'
abstract:
- lang: eng
text: As an important plant hormone to regulate growth and development, auxin has
been investigated for more than a century. It had been clearly demonstrated and
well-accepted that the intracellular auxin receptors, TIR1/AFBs, are F-box proteins
mediating transcriptional auxin signaling by their E3 ubiquitin ligase activity,
which targets and sends for degradation the Aux/IAA transcriptional repressors.
The recent discovery of adenylate cyclase (AC) and guanylate cyclase (GC) activities
for TIR1/AFBs open entirely new perspectives on how auxin signaling can operate.
This chapter traces back the history of how canonical transcriptional auxin signaling
was established and introduces the discovery of the TIR1/AFBs-mediated nontranscriptional
signaling branch. Finally, the current understanding and open questions of how
TIR1/AFBs’ AC and GC activities contribute to the transcriptional and nontranscriptional
auxin signaling are discussed, highlighting the possibility that cyclic adenosine
monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) act as second messengers
in auxin signal transduction.
alternative_title:
- Foundations and Frontiers in Enzymology
article_processing_charge: No
author:
- first_name: Linlin
full_name: Qi, Linlin
last_name: Qi
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Qi L, Friml J. Nucleotidyl cyclase activities of TIR1/AFB auxin receptors:
new insights into the mechanism of auxin signaling. In: Irving H, Gehring C, Wong
A, eds. Cryptic Enzymes and Moonlighting Proteins. Elsevier; 2025:299-322.
doi:10.1016/b978-0-443-15719-6.00015-5'
apa: 'Qi, L., & Friml, J. (2025). Nucleotidyl cyclase activities of TIR1/AFB
auxin receptors: new insights into the mechanism of auxin signaling. In H. Irving,
C. Gehring, & A. Wong (Eds.), Cryptic Enzymes and Moonlighting Proteins
(pp. 299–322). Elsevier. https://doi.org/10.1016/b978-0-443-15719-6.00015-5'
chicago: 'Qi, Linlin, and Jiří Friml. “Nucleotidyl Cyclase Activities of TIR1/AFB
Auxin Receptors: New Insights into the Mechanism of Auxin Signaling.” In Cryptic
Enzymes and Moonlighting Proteins, edited by Helen Irving, Chris Gehring,
and Aloysius Wong, 299–322. Elsevier, 2025. https://doi.org/10.1016/b978-0-443-15719-6.00015-5.'
ieee: 'L. Qi and J. Friml, “Nucleotidyl cyclase activities of TIR1/AFB auxin receptors:
new insights into the mechanism of auxin signaling,” in Cryptic Enzymes and
Moonlighting Proteins, H. Irving, C. Gehring, and A. Wong, Eds. Elsevier,
2025, pp. 299–322.'
ista: 'Qi L, Friml J. 2025.Nucleotidyl cyclase activities of TIR1/AFB auxin receptors:
new insights into the mechanism of auxin signaling. In: Cryptic Enzymes and Moonlighting
Proteins. Foundations and Frontiers in Enzymology, , 299–322.'
mla: 'Qi, Linlin, and Jiří Friml. “Nucleotidyl Cyclase Activities of TIR1/AFB Auxin
Receptors: New Insights into the Mechanism of Auxin Signaling.” Cryptic Enzymes
and Moonlighting Proteins, edited by Helen Irving et al., Elsevier, 2025,
pp. 299–322, doi:10.1016/b978-0-443-15719-6.00015-5.'
short: L. Qi, J. Friml, in:, H. Irving, C. Gehring, A. Wong (Eds.), Cryptic Enzymes
and Moonlighting Proteins, Elsevier, 2025, pp. 299–322.
date_created: 2026-02-16T15:53:52Z
date_published: 2025-05-02T00:00:00Z
date_updated: 2026-02-17T13:28:38Z
day: '02'
department:
- _id: JiFr
doi: 10.1016/b978-0-443-15719-6.00015-5
editor:
- first_name: Helen
full_name: Irving, Helen
last_name: Irving
- first_name: Chris
full_name: Gehring, Chris
last_name: Gehring
- first_name: Aloysius
full_name: Wong, Aloysius
last_name: Wong
language:
- iso: eng
month: '05'
oa_version: None
page: 299-322
publication: Cryptic Enzymes and Moonlighting Proteins
publication_identifier:
isbn:
- '9780443157196'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nucleotidyl cyclase activities of TIR1/AFB auxin receptors: new insights into
the mechanism of auxin signaling'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21256'
abstract:
- lang: eng
text: Collagen IV is one of the main components of the basement membrane, a layer
of material that lines the majority of tissues in multicellular organisms. Collagen
IV molecules assemble into networks, providing stiffness and elasticity to tissues
and informing cell and organ shape, especially during development. In this work,
we develop two coarse-grained models for collagen IV molecules that retain biochemical
bond specificity and coarse grain at different length scales. Through molecular-dynamics
simulations, we test the assembly and mechanics of the resulting networks and
measure their response to strain in terms of stress, microscopic alignment, and
bond dynamics. Within the basement membrane, collagen IV networks rearrange by
molecule turnover, which affects tissue organization and can be linked with enzyme
activity. Here we explore network rearrangements via bond remodeling, the process
of breaking and remaking of bonds between network molecules. We then investigate
the effects of active (enzymatic) bond remodeling. We find that this nonequilibrium
remodeling allows a network to keep its integrity under strain, while relaxing
fully over a variety of timescales, a dynamic response that is unavailable to
networks undergoing equilibrium remodeling.
acknowledgement: This work received funding from the European Research Council under
the European Union's Horizon 2020 research and innovation program through Grant
Agreement No. 802960 (B.M., V.S., I.P., and A.Š.), the European Union's Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 101034413 (I.P.), the NOMIS Foundation (F.P.-V.), the National Centre for the
Replacement, Refinement and Reduction of Animals in Research Grant No. NC/T002425/1
(N.K.), Leverhulme Trust project Grant No. RPG-2020-068 (N.K.), MRC Fellowship No.
MR/W027437/1 (Y.M.), a Lister Institute Research Prize (Y.M.) and EMBO Young Investigator
Programme (Y.M. and A.Š.).
article_number: '033019'
article_processing_charge: Yes
article_type: original
author:
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
orcid: 0000-0003-3441-1337
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Eryk
full_name: Ratajczyk, Eryk
last_name: Ratajczyk
- first_name: Fernanda L
full_name: Perez Verdugo, Fernanda L
id: 4ecec223-9070-11ef-a0a9-bc76077bea8d
last_name: Perez Verdugo
- first_name: Nargess
full_name: Khalilgharibi, Nargess
last_name: Khalilgharibi
- first_name: Yanlan
full_name: Mao, Yanlan
last_name: Mao
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Meadowcroft B, Sorichetti V, Ratajczyk E, et al. Nonequilibrium remodeling
of collagen IV networks in Silico. PRX Life. 2025;3. doi:10.1103/gdd5-rnh7
apa: Meadowcroft, B., Sorichetti, V., Ratajczyk, E., Perez Verdugo, F. L., Khalilgharibi,
N., Mao, Y., … Šarić, A. (2025). Nonequilibrium remodeling of collagen IV networks
in Silico. PRX Life. American Physical Society. https://doi.org/10.1103/gdd5-rnh7
chicago: Meadowcroft, Billie, Valerio Sorichetti, Eryk Ratajczyk, Fernanda L Perez
Verdugo, Nargess Khalilgharibi, Yanlan Mao, Ivan Palaia, and Anđela Šarić. “Nonequilibrium
Remodeling of Collagen IV Networks in Silico.” PRX Life. American Physical
Society, 2025. https://doi.org/10.1103/gdd5-rnh7.
ieee: B. Meadowcroft et al., “Nonequilibrium remodeling of collagen IV networks
in Silico,” PRX Life, vol. 3. American Physical Society, 2025.
ista: Meadowcroft B, Sorichetti V, Ratajczyk E, Perez Verdugo FL, Khalilgharibi
N, Mao Y, Palaia I, Šarić A. 2025. Nonequilibrium remodeling of collagen IV networks
in Silico. PRX Life. 3, 033019.
mla: Meadowcroft, Billie, et al. “Nonequilibrium Remodeling of Collagen IV Networks
in Silico.” PRX Life, vol. 3, 033019, American Physical Society, 2025,
doi:10.1103/gdd5-rnh7.
short: B. Meadowcroft, V. Sorichetti, E. Ratajczyk, F.L. Perez Verdugo, N. Khalilgharibi,
Y. Mao, I. Palaia, A. Šarić, PRX Life 3 (2025).
corr_author: '1'
date_created: 2026-02-16T15:55:03Z
date_published: 2025-09-05T00:00:00Z
date_updated: 2026-02-17T13:37:38Z
day: '05'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1103/gdd5-rnh7
ec_funded: 1
file:
- access_level: open_access
checksum: 04cae5231d97e533145c493880fadbd9
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T13:36:01Z
date_updated: 2026-02-17T13:36:01Z
file_id: '21308'
file_name: 2025_PRXLife_Meadowcroft.pdf
file_size: 2277704
relation: main_file
success: 1
file_date_updated: 2026-02-17T13:36:01Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 349b6ff1-11ca-11ed-8bc3-f006047c2eeb
name: EMBO Young Investigator Program - Andela Saric
publication: PRX Life
publication_identifier:
eissn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Nonequilibrium remodeling of collagen IV networks in Silico
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: 3
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21257'
abstract:
- lang: eng
text: 'We investigate the problem of accurate sparse fine-tuning of large language
models (LLMs), that is, fine-tuning pre-trained LLMs on specialized tasks, while
inducing sparsity in their weights. Our work is motivated by experiments showing
that standard loss-based fine-tuning methods are not able to achieve high accuracy
in this setting, especially at high sparsity targets. To address this issue, we
perform a detailed study of knowledge distillation losses for fine-tuning of sparse
models. We determine an L2-based distillation approach that we term ‘SquareHead’,
which enables accurate recovery even at higher sparsities. Investigating the question
of efficient inference, we show that sparse LLMs can be executed faster by taking
advantage of sparsity. Specifically, we exhibit end-to-end results showing speedups
enabled by sparsity, while recovering accuracy, on the following models and tasks,
respectively: T5 for language translation, Whisper for speech translation, and
open GPT-type models such as the Mosaic Pre-Trained Transformer (MPT) and Llama-2
models for text generation. In particular, for popular generative tasks, we show
for the first time that sparse fine-tuning can reach 75% sparsity without drops
in accuracy, and provide notable end-to-end speedups for inference on CPUs. Moreover,
we also highlight that sparsity is compatible with other compression approaches,
such as quantization.'
acknowledgement: We would like to thank Eugenia Iofinova for useful comments on an
earlier version of this draft, and Artur Niederfahrenhorst for useful suggestions
regarding fine-tuning on the GSM8k dataset.
alternative_title:
- 'Machine Translation: Technologies and Applications'
article_processing_charge: No
arxiv: 1
author:
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- first_name: Denis
full_name: Kuznedelev, Denis
last_name: Kuznedelev
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Michael
full_name: Goinv, Michael
last_name: Goinv
- first_name: Shubhra
full_name: Pandit, Shubhra
last_name: Pandit
- first_name: Abhinav
full_name: Agarwalla, Abhinav
last_name: Agarwalla
- first_name: Tuan
full_name: Nguyen, Tuan
last_name: Nguyen
- first_name: Alexandre
full_name: Marques, Alexandre
last_name: Marques
- first_name: Mark
full_name: Kurtz, Mark
last_name: Kurtz
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Kurtic E, Kuznedelev D, Frantar E, et al. Sparse Fine-Tuning for Inference
Acceleration of Large Language Models. In: Passban P, Way A, Rezagholizadeh M,
eds. Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques.
Springer Nature; 2025:83-97. doi:10.1007/978-3-031-85747-8_6'
apa: Kurtic, E., Kuznedelev, D., Frantar, E., Goinv, M., Pandit, S., Agarwalla,
A., … Alistarh, D.-A. (2025). Sparse Fine-Tuning for Inference Acceleration of
Large Language Models. In P. Passban, A. Way, & M. Rezagholizadeh (Eds.),
Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques
(pp. 83–97). Springer Nature. https://doi.org/10.1007/978-3-031-85747-8_6
chicago: Kurtic, Eldar, Denis Kuznedelev, Elias Frantar, Michael Goinv, Shubhra
Pandit, Abhinav Agarwalla, Tuan Nguyen, Alexandre Marques, Mark Kurtz, and Dan-Adrian
Alistarh. “Sparse Fine-Tuning for Inference Acceleration of Large Language Models.”
In Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques,
edited by Peyman Passban, Andy Way, and Mehdi Rezagholizadeh, 83–97. Springer
Nature, 2025. https://doi.org/10.1007/978-3-031-85747-8_6.
ieee: E. Kurtic et al., “Sparse Fine-Tuning for Inference Acceleration of
Large Language Models,” in Enhancing LLM Performance. Efficacy, Fine-Tuning,
and Inference Techniques, P. Passban, A. Way, and M. Rezagholizadeh, Eds.
Springer Nature, 2025, pp. 83–97.
ista: 'Kurtic E, Kuznedelev D, Frantar E, Goinv M, Pandit S, Agarwalla A, Nguyen
T, Marques A, Kurtz M, Alistarh D-A. 2025.Sparse Fine-Tuning for Inference Acceleration
of Large Language Models. In: Enhancing LLM Performance. Efficacy, Fine-Tuning,
and Inference Techniques. Machine Translation: Technologies and Applications,
, 83–97.'
mla: Kurtic, Eldar, et al. “Sparse Fine-Tuning for Inference Acceleration of Large
Language Models.” Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference
Techniques, edited by Peyman Passban et al., Springer Nature, 2025, pp. 83–97,
doi:10.1007/978-3-031-85747-8_6.
short: E. Kurtic, D. Kuznedelev, E. Frantar, M. Goinv, S. Pandit, A. Agarwalla,
T. Nguyen, A. Marques, M. Kurtz, D.-A. Alistarh, in:, P. Passban, A. Way, M. Rezagholizadeh
(Eds.), Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques,
Springer Nature, 2025, pp. 83–97.
corr_author: '1'
date_created: 2026-02-16T15:57:53Z
date_published: 2025-07-05T00:00:00Z
date_updated: 2026-02-19T09:26:54Z
day: '05'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-85747-8_6
editor:
- first_name: Peyman
full_name: Passban, Peyman
last_name: Passban
- first_name: Andy
full_name: Way, Andy
last_name: Way
- first_name: Mehdi
full_name: Rezagholizadeh, Mehdi
last_name: Rezagholizadeh
external_id:
arxiv:
- '2310.06927'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.06927
month: '07'
oa: 1
oa_version: Preprint
page: 83-97
publication: Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques
publication_identifier:
eisbn:
- '9783031857478'
eissn:
- 2522-803X
isbn:
- '9783031857461'
issn:
- 2522-8021
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Sparse Fine-Tuning for Inference Acceleration of Large Language Models
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21262'
abstract:
- lang: eng
text: "Continuous Group Key Agreement (CGKA) is the primitive underlying secure
group messaging. It allows a large group of N users to maintain a shared secret
key that is frequently rotated by the\r\ngroup members in order to achieve forward
secrecy and post compromise security. The group messaging scheme Messaging Layer
Security (MLS) standardized by the IETF makes use of a CGKA called TreeKEM which
arranges the N group members in a binary tree. Here, each node is associated with
a public-key, each user is assigned one of the leaves, and a user knows the corresponding
secret keys from their leaf to the root. To update the key material known to them,
a user must just replace keys at log(N) nodes, which requires them to create and
upload log(N) ciphertexts. Such updates must be processed sequentially by all
users, which for large groups is impractical. To allow for concurrent updates,
TreeKEM uses the “propose and commit” paradigm, where multiple users can concurrently
propose to update (by just sampling a fresh leaf key), and a single user can then
commit to all proposals at once. Unfortunately, this process destroys the binary
tree structure as the tree gets pruned and some nodes must be “blanked” at the
cost of increasing the in-degree of others, which makes the commit operation,
as well as, future commits more costly. In the worst case, the update cost (in
terms of uploaded ciphertexts) per user can grow from log(N) to Ω(N). In this
work we provide two main contributions. First, we show that MLS’ communication
complexity is bad not only in the worst case but also if the proposers and committers
are chosen at random: even if there’s just one update proposal for every commit
the expected cost is already over √N, and it approaches N as this ratio changes
towards more proposals. Our second contribution is a new variant of propose and
commit for\r\nTreeKEM which for moderate amounts of update proposals per commit
provably achieves an update cost of Θ(log(N)) assuming the proposers and committers
are chosen at random."
acknowledgement: B. Auerbach and B. Erol—Conducted part of this work at ISTA.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- first_name: Boran
full_name: Erol, Boran
last_name: Erol
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. Continuous group-key agreement:
Concurrent updates without pruning. In: 45th Annual International Cryptology
Conference. Vol 16007. Springer Nature; 2025:141-172. doi:10.1007/978-3-032-01913-4_5'
apa: 'Auerbach, B., Cueto Noval, M., Erol, B., & Pietrzak, K. Z. (2025). Continuous
group-key agreement: Concurrent updates without pruning. In 45th Annual International
Cryptology Conference (Vol. 16007, pp. 141–172). Santa Barbara, CA, United
States: Springer Nature. https://doi.org/10.1007/978-3-032-01913-4_5'
chicago: 'Auerbach, Benedikt, Miguel Cueto Noval, Boran Erol, and Krzysztof Z Pietrzak.
“Continuous Group-Key Agreement: Concurrent Updates without Pruning.” In 45th
Annual International Cryptology Conference, 16007:141–72. Springer Nature,
2025. https://doi.org/10.1007/978-3-032-01913-4_5.'
ieee: 'B. Auerbach, M. Cueto Noval, B. Erol, and K. Z. Pietrzak, “Continuous group-key
agreement: Concurrent updates without pruning,” in 45th Annual International
Cryptology Conference, Santa Barbara, CA, United States, 2025, vol. 16007,
pp. 141–172.'
ista: 'Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. 2025. Continuous group-key
agreement: Concurrent updates without pruning. 45th Annual International Cryptology
Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 16007, 141–172.'
mla: 'Auerbach, Benedikt, et al. “Continuous Group-Key Agreement: Concurrent Updates
without Pruning.” 45th Annual International Cryptology Conference, vol.
16007, Springer Nature, 2025, pp. 141–72, doi:10.1007/978-3-032-01913-4_5.'
short: B. Auerbach, M. Cueto Noval, B. Erol, K.Z. Pietrzak, in:, 45th Annual International
Cryptology Conference, Springer Nature, 2025, pp. 141–172.
conference:
end_date: 2025-08-21
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2025-08-17
date_created: 2026-02-17T07:41:04Z
date_published: 2025-08-17T00:00:00Z
date_updated: 2026-02-18T07:36:42Z
day: '17'
department:
- _id: KrPi
doi: 10.1007/978-3-032-01913-4_5
intvolume: ' 16007'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2025/1035
month: '08'
oa: 1
oa_version: Preprint
page: 141-172
publication: 45th Annual International Cryptology Conference
publication_identifier:
eisbn:
- '9783032019134'
eissn:
- 1611-3349
isbn:
- '9783032019127'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Continuous group-key agreement: Concurrent updates without pruning'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16007
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21268'
abstract:
- lang: eng
text: "We consider multiple-environment Markov decision processes (MEMDP), which
consist of a finite set of MDPs over the same state space, representing different
scenarios of transition structure and probability. The value of a strategy is
the probability to satisfy the objective, here a parity objective, in the worst-case
scenario, and the value of an MEMDP is the supremum of the values achievable by
a strategy.\r\nWe show that deciding whether the value is 1 is a PSPACE-complete
problem, and even in P when the number of environments is fixed, along with new
insights to the almost-sure winning problem, which is to decide if there exists
a strategy with value 1. Pure strategies are sufficient for theses problems, whereas
randomization is necessary in general when the value is smaller than 1. We present
an algorithm to approximate the value, running in double exponential space. Our
results are in contrast to the related model of partially-observable MDPs where
all these problems are known to be undecidable."
acknowledgement: "Krishnendu Chatterjee: ERC CoG 863818 (ForM-SMArt) and Austrian
Science Fund\r\n(FWF) 10.55776/COE12. Jean-François Raskin: PDR Weave project FORM-LEARN-POMDP
funded by FNRS and DFG, and the support of the Fondation ULB. Ocan Sankur: ANR BisoUS
(ANR-22-CE48-0012) and ANR EpiRL (ANR-22-CE23-0029)."
alternative_title:
- LIPIcs
article_number: '150'
article_processing_charge: No
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Jean-Francois
full_name: Raskin, Jean-Francois
last_name: Raskin
- first_name: Ocan
full_name: Sankur, Ocan
last_name: Sankur
citation:
ama: 'Chatterjee K, Doyen L, Raskin J-F, Sankur O. The value problem for multiple-environment
MDPs with parity objective. In: 52nd International Colloquium on Automata,
Languages, and Programming. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2025. doi:10.4230/LIPIcs.ICALP.2025.150'
apa: 'Chatterjee, K., Doyen, L., Raskin, J.-F., & Sankur, O. (2025). The value
problem for multiple-environment MDPs with parity objective. In 52nd International
Colloquium on Automata, Languages, and Programming. Aarhus, Denmark: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2025.150'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Jean-Francois Raskin, and Ocan Sankur.
“The Value Problem for Multiple-Environment MDPs with Parity Objective.” In 52nd
International Colloquium on Automata, Languages, and Programming. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2025. https://doi.org/10.4230/LIPIcs.ICALP.2025.150.
ieee: K. Chatterjee, L. Doyen, J.-F. Raskin, and O. Sankur, “The value problem for
multiple-environment MDPs with parity objective,” in 52nd International Colloquium
on Automata, Languages, and Programming, Aarhus, Denmark, 2025.
ista: 'Chatterjee K, Doyen L, Raskin J-F, Sankur O. 2025. The value problem for
multiple-environment MDPs with parity objective. 52nd International Colloquium
on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming,
LIPIcs, , 150.'
mla: Chatterjee, Krishnendu, et al. “The Value Problem for Multiple-Environment
MDPs with Parity Objective.” 52nd International Colloquium on Automata, Languages,
and Programming, 150, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025,
doi:10.4230/LIPIcs.ICALP.2025.150.
short: K. Chatterjee, L. Doyen, J.-F. Raskin, O. Sankur, in:, 52nd International
Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2025.
conference:
end_date: 2025-07-11
location: Aarhus, Denmark
name: 'ICALP: Automata, Languages and Programming'
start_date: 2025-07-08
corr_author: '1'
date_created: 2026-02-17T07:49:17Z
date_published: 2025-07-30T00:00:00Z
date_updated: 2026-02-18T07:53:26Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2025.150
ec_funded: 1
external_id:
arxiv:
- '2504.15960'
file:
- access_level: open_access
checksum: 4477a7fd4fbf0ba6c8e9b15683b5a6b8
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T07:50:56Z
date_updated: 2026-02-18T07:50:56Z
file_id: '21313'
file_name: 2025_LIPIcs_Chatterjee.pdf
file_size: 1075724
relation: main_file
success: 1
file_date_updated: 2026-02-18T07:50:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
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: 52nd International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959773720'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: The value problem for multiple-environment MDPs with parity objective
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21269'
abstract:
- lang: eng
text: The spatial organization of chromatin within the nucleus plays a crucial role
in gene expression and genome function. However, the quantitative relationship
between this organization and nuclear biochemical processes remains under debate.
In this study, we present a graph-based generative model, bioSBM, designed to
capture long-range chromatin interaction patterns from Hi-C data and, importantly,
simultaneously link these patterns to biochemical features. Applying bioSBM to
Hi-C maps of the GM12878 lymphoblastoid cell line, we identified a latent structure
of chromatin interactions, revealing seven distinct communities that strongly
align with known biological annotations. Additionally, we infer a linear transformation
that maps biochemical observables, such as histone marks, to the parameters of
the generative graph model, enabling accurate genome-wide predictions of chromatin
contact maps on out-of-sample data, both within the same cell line and on the
completely unseen HCT116 cell line under RAD21 depletion. These findings highlight
bioSBM's potential as a powerful tool for elucidating the relationship between
biochemistry and chromatin architecture and predicting long-range genome organization
from independent biochemical data.
acknowledgement: G.S. acknowledges co-funding from Next Generation EU, in the context
of the National Recovery and Resilience Plan, Investment PE1 - Project FAIR “Future
Artificial Intelligence Research”. This resource was co-financed by the Next Generation
EU [DM 1555 del 11.10.22]. A.R. acknowledges financial support from PNRR Grant CN
00000013 CN-HPC, M4C2I1.4, spoke 7, funded by Next Generation EU.
article_number: '043006'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Chen Y
full_name: Zhang, Chen Y
id: 81b43fb8-c9d5-11ef-bf68-ade532a1f204
last_name: Zhang
- first_name: Angelo
full_name: Rosa, Angelo
last_name: Rosa
- first_name: Guido
full_name: Sanguinetti, Guido
last_name: Sanguinetti
citation:
ama: 'Zhang CY, Rosa A, Sanguinetti G. bioSBM: A random graph model to integrate
epigenomic data in chromatin structure prediction. PRX Life. 2025;3(4).
doi:10.1103/gy1p-4256'
apa: 'Zhang, C. Y., Rosa, A., & Sanguinetti, G. (2025). bioSBM: A random graph
model to integrate epigenomic data in chromatin structure prediction. PRX Life.
American Physical Society. https://doi.org/10.1103/gy1p-4256'
chicago: 'Zhang, Chen Y, Angelo Rosa, and Guido Sanguinetti. “BioSBM: A Random Graph
Model to Integrate Epigenomic Data in Chromatin Structure Prediction.” PRX
Life. American Physical Society, 2025. https://doi.org/10.1103/gy1p-4256.'
ieee: 'C. Y. Zhang, A. Rosa, and G. Sanguinetti, “bioSBM: A random graph model to
integrate epigenomic data in chromatin structure prediction,” PRX Life,
vol. 3, no. 4. American Physical Society, 2025.'
ista: 'Zhang CY, Rosa A, Sanguinetti G. 2025. bioSBM: A random graph model to integrate
epigenomic data in chromatin structure prediction. PRX Life. 3(4), 043006.'
mla: 'Zhang, Chen Y., et al. “BioSBM: A Random Graph Model to Integrate Epigenomic
Data in Chromatin Structure Prediction.” PRX Life, vol. 3, no. 4, 043006,
American Physical Society, 2025, doi:10.1103/gy1p-4256.'
short: C.Y. Zhang, A. Rosa, G. Sanguinetti, PRX Life 3 (2025).
corr_author: '1'
date_created: 2026-02-17T07:53:01Z
date_published: 2025-10-21T00:00:00Z
date_updated: 2026-02-18T08:01:00Z
day: '21'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1103/gy1p-4256
external_id:
arxiv:
- '2409.14425'
file:
- access_level: open_access
checksum: 76ddfee3efdb4c9d085059b5a142ed78
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T07:57:39Z
date_updated: 2026-02-18T07:57:39Z
file_id: '21314'
file_name: 2025_PRXLife_Zhang.pdf
file_size: 1888053
relation: main_file
success: 1
file_date_updated: 2026-02-18T07:57:39Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PRX Life
publication_identifier:
issn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'bioSBM: A random graph model to integrate epigenomic data in chromatin structure
prediction'
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: 3
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21270'
abstract:
- lang: eng
text: "The one-dimensional Fröhlich model describing the motion of a single electron
interacting with optical phonons is a paradigmatic model of quantum many-body
physics. We predict the existence of an arbitrarily large number of bound excited
states in the strong-coupling limit and calculate their excitation energies. Numerical
simulations of a discretized model demonstrate the complete amelioration of the
projector Monte Carlo sign problem by walker annihilation in an infinite Hilbert
space. They reveal the threshold for the occurrence of the first bound excited
states at a value of \U0001D6FC≈1.73 for the dimensionless coupling constant.
This puts the threshold into the regime of intermediate interaction strength.
We find a significant spectral weight and increased phonon number of the bound
excited state at threshold."
acknowledgement: We are grateful to Dmytro Kolisnyk for his help in working out the
spectrum of the Hessian. This work was supported by the Marsden Fund of New Zealand
(Contract No. MAU2007) from government funding administered by the Royal Society
Te Apārangi and by a summer scholarship from Te Whai Ao – Dodd-Walls Centre for
Photonic and Quantum Technologies and the Physics Department, University of Auckland.
We acknowledge support by the New Zealand eScience Infrastructure (NeSI) high-performance
computing facilities in the form of a merit project allocation.
article_number: '184312'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Taylor, J.
last_name: Taylor
- first_name: M.
full_name: Čufar, M.
last_name: Čufar
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: E.
full_name: Pahl, E.
last_name: Pahl
- first_name: J.
full_name: Brand, J.
last_name: Brand
citation:
ama: Taylor J, Čufar M, Mitrouskas DJ, Seiringer R, Pahl E, Brand J. Bound excited
states of Fröhlich polarons in one dimension. Physical Review B. 2025;112(18).
doi:10.1103/s9p9-jflq
apa: Taylor, J., Čufar, M., Mitrouskas, D. J., Seiringer, R., Pahl, E., & Brand,
J. (2025). Bound excited states of Fröhlich polarons in one dimension. Physical
Review B. American Physical Society. https://doi.org/10.1103/s9p9-jflq
chicago: Taylor, J., M. Čufar, David Johannes Mitrouskas, Robert Seiringer, E. Pahl,
and J. Brand. “Bound Excited States of Fröhlich Polarons in One Dimension.” Physical
Review B. American Physical Society, 2025. https://doi.org/10.1103/s9p9-jflq.
ieee: J. Taylor, M. Čufar, D. J. Mitrouskas, R. Seiringer, E. Pahl, and J. Brand,
“Bound excited states of Fröhlich polarons in one dimension,” Physical Review
B, vol. 112, no. 18. American Physical Society, 2025.
ista: Taylor J, Čufar M, Mitrouskas DJ, Seiringer R, Pahl E, Brand J. 2025. Bound
excited states of Fröhlich polarons in one dimension. Physical Review B. 112(18),
184312.
mla: Taylor, J., et al. “Bound Excited States of Fröhlich Polarons in One Dimension.”
Physical Review B, vol. 112, no. 18, 184312, American Physical Society,
2025, doi:10.1103/s9p9-jflq.
short: J. Taylor, M. Čufar, D.J. Mitrouskas, R. Seiringer, E. Pahl, J. Brand, Physical
Review B 112 (2025).
date_created: 2026-02-17T07:56:20Z
date_published: 2025-11-18T00:00:00Z
date_updated: 2026-02-18T08:23:59Z
day: '18'
department:
- _id: RoSe
doi: 10.1103/s9p9-jflq
external_id:
arxiv:
- '2506.02440 '
intvolume: ' 112'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.48550/arXiv.2506.02440 '
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bound excited states of Fröhlich polarons in one dimension
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21271'
abstract:
- lang: eng
text: For general non-Hermitian large random matrices X and deterministic deformation
matrices A, we prove that the local eigenvalue statistics of A+X close to the
typical edge points of its spectrum are universal. Furthermore, we show that,
under natural assumptions, on A the spectrum of A+X does not have outliers at
a distance larger than the natural fluctuation scale of the eigenvalues. As a
consequence, the number of eigenvalues in each component of Spec(A+X) is deterministic.
acknowledgement: The authors would like to thank the anonymous referee for providing
helpful comments and suggestions. We also thank Joscha Henheik and Volodymyr Riabov
for pointing out a gap in an earlier version of the proof of equation (3.18). The
first, third, and fourth authors are supported by ERC Advanced Grant “RMTBeyond”
No. 101020331.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Andrew J
full_name: Campbell, Andrew J
id: 582b06a9-1f1c-11ee-b076-82ffce00dde4
last_name: Campbell
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Campbell AJ, Cipolloni G, Erdös L, Ji HC. On the spectral edge of non-Hermitian
random matrices. The Annals of Probability. 2025;53(6):2256-2308. doi:10.1214/25-aop1761
apa: Campbell, A. J., Cipolloni, G., Erdös, L., & Ji, H. C. (2025). On the spectral
edge of non-Hermitian random matrices. The Annals of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/25-aop1761
chicago: Campbell, Andrew J, Giorgio Cipolloni, László Erdös, and Hong Chang Ji.
“On the Spectral Edge of Non-Hermitian Random Matrices.” The Annals of Probability.
Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/25-aop1761.
ieee: A. J. Campbell, G. Cipolloni, L. Erdös, and H. C. Ji, “On the spectral edge
of non-Hermitian random matrices,” The Annals of Probability, vol. 53,
no. 6. Institute of Mathematical Statistics, pp. 2256–2308, 2025.
ista: Campbell AJ, Cipolloni G, Erdös L, Ji HC. 2025. On the spectral edge of non-Hermitian
random matrices. The Annals of Probability. 53(6), 2256–2308.
mla: Campbell, Andrew J., et al. “On the Spectral Edge of Non-Hermitian Random Matrices.”
The Annals of Probability, vol. 53, no. 6, Institute of Mathematical Statistics,
2025, pp. 2256–308, doi:10.1214/25-aop1761.
short: A.J. Campbell, G. Cipolloni, L. Erdös, H.C. Ji, The Annals of Probability
53 (2025) 2256–2308.
corr_author: '1'
date_created: 2026-02-17T07:58:20Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-02-18T08:35:38Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/25-aop1761
ec_funded: 1
external_id:
arxiv:
- '2404.17512'
intvolume: ' 53'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.17512
month: '11'
oa: 1
oa_version: Preprint
page: 2256-2308
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: The Annals of Probability
publication_identifier:
eissn:
- 2168-894X
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: On the spectral edge of non-Hermitian random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21272'
abstract:
- lang: eng
text: Finding the ground state of Ising spin glasses is notoriously difficult due
to disorder and frustration. Often, this challenge is framed as a combinatorial
optimization problem, for which a common strategy employs simulated annealing,
a Monte Carlo (MC)-based algorithm that updates spins one at a time. Yet, these
localized updates can cause the system to become trapped in local minima. Cluster
algorithms (CAs) were developed to address this limitation and have demonstrated
considerable success in studying ferromagnetic systems; however, they tend to
encounter percolation issues when applied to generic spin glasses. In this work,
we introduce a novel CA designed to tackle these challenges by leveraging precomputed
two-point correlations, aiming solve combinatorial optimization problems in the
form of Max-Cut more efficiently. In our approach, clusters are formed probabilistically
based on these correlations. Various classical and quantum algorithms can be employed
to generate correlations that embody information about the energy landscape of
the problem. By utilizing this information, the algorithm aims to identify groups
of spins whose simultaneous flipping induces large transitions in configuration
space with high acceptance probability - even at low energy levels - thereby escaping
local minima more effectively. Notably, clusters generated using correlations
from the Quantum Approximate Optimization Algorithm exhibit high acceptance rates
at low temperatures. These acceptance rates often increase with circuit depth,
accelerating the algorithm and enabling more efficient exploration of the solution
space.
acknowledgement: "P.J.E was partially funded by the German BMWK project QCHALLenge
(Grant No. 01MQ22008B).\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Peter J.
full_name: Eder, Peter J.
last_name: Eder
- first_name: Aron
full_name: Kerschbaumer, Aron
id: ade85a9c-3200-11ee-973b-91c1eb240410
last_name: Kerschbaumer
orcid: 0009-0002-2370-8661
- first_name: Jernej Rudi
full_name: Finžgar, Jernej Rudi
last_name: Finžgar
- 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: Martin J. A.
full_name: Schuetz, Martin J. A.
last_name: Schuetz
- first_name: Helmut G.
full_name: Katzgraber, Helmut G.
last_name: Katzgraber
- first_name: Sarah
full_name: Braun, Sarah
last_name: Braun
- first_name: Christian B.
full_name: Mendl, Christian B.
last_name: Mendl
citation:
ama: 'Eder PJ, Kerschbaumer A, Finžgar JR, et al. Quantum-guided cluster algorithms
for combinatorial optimization. In: 2025 IEEE International Conference on Quantum
Computing and Engineering. IEEE; 2025. doi:10.1109/qce65121.2025.00033'
apa: 'Eder, P. J., Kerschbaumer, A., Finžgar, J. R., Medina Ramos, R. A., Schuetz,
M. J. A., Katzgraber, H. G., … Mendl, C. B. (2025). Quantum-guided cluster algorithms
for combinatorial optimization. In 2025 IEEE International Conference on Quantum
Computing and Engineering. Albuquerque, NM, United States: IEEE. https://doi.org/10.1109/qce65121.2025.00033'
chicago: Eder, Peter J., Aron Kerschbaumer, Jernej Rudi Finžgar, Raimel A Medina
Ramos, Martin J. A. Schuetz, Helmut G. Katzgraber, Sarah Braun, and Christian
B. Mendl. “Quantum-Guided Cluster Algorithms for Combinatorial Optimization.”
In 2025 IEEE International Conference on Quantum Computing and Engineering.
IEEE, 2025. https://doi.org/10.1109/qce65121.2025.00033.
ieee: P. J. Eder et al., “Quantum-guided cluster algorithms for combinatorial
optimization,” in 2025 IEEE International Conference on Quantum Computing and
Engineering, Albuquerque, NM, United States, 2025.
ista: 'Eder PJ, Kerschbaumer A, Finžgar JR, Medina Ramos RA, Schuetz MJA, Katzgraber
HG, Braun S, Mendl CB. 2025. Quantum-guided cluster algorithms for combinatorial
optimization. 2025 IEEE International Conference on Quantum Computing and Engineering.
QCE: International Conference on Quantum Computing and Engineering.'
mla: Eder, Peter J., et al. “Quantum-Guided Cluster Algorithms for Combinatorial
Optimization.” 2025 IEEE International Conference on Quantum Computing and
Engineering, IEEE, 2025, doi:10.1109/qce65121.2025.00033.
short: P.J. Eder, A. Kerschbaumer, J.R. Finžgar, R.A. Medina Ramos, M.J.A. Schuetz,
H.G. Katzgraber, S. Braun, C.B. Mendl, in:, 2025 IEEE International Conference
on Quantum Computing and Engineering, IEEE, 2025.
conference:
end_date: 2025-09-05
location: Albuquerque, NM, United States
name: 'QCE: International Conference on Quantum Computing and Engineering'
start_date: 2025-08-30
corr_author: '1'
date_created: 2026-02-17T08:00:17Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-02-18T08:45:56Z
day: '01'
department:
- _id: MaSe
doi: 10.1109/qce65121.2025.00033
external_id:
arxiv:
- '2508.10656'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2508.10656
month: '09'
oa: 1
oa_version: Preprint
publication: 2025 IEEE International Conference on Quantum Computing and Engineering
publication_identifier:
eisbn:
- '9798331557362'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Quantum-guided cluster algorithms for combinatorial optimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...