---
OA_place: publisher
OA_type: hybrid
_id: '20866'
abstract:
- lang: eng
text: In this work, we present hypernode automata as a specification formalism for
hyperproperties of systems whose executions may be misaligned among themselves,
such as concurrent systems. These automata consist of nodes labeled with hypernode
logic formulas and transitions marked with synchronizing actions. Hypernode logic
formulas establish relations between sequences of variable values among different
system executions. This logic enables both synchronous and asynchronous analysis
of traces. In its asynchronous view on execution traces, hypernode formulas establish
relations on the order of value changes for each variable without correlating
their timing. In both views, the analysis of different execution traces is synchronized
through the transitions of hypernode automata. By combining logic’s declarative
nature with automata’s procedural power, hypernode automata seamlessly integrate
asynchronicity requirements at the node level with synchronicity between node
transitions. We show that the model-checking problem for hypernode automata is
decidable for specifications where each node specifies either a synchronous or
an asynchronous requirement for the system’s executions, but not both.
acknowledgement: This work was supported in part by the Austrian Science Fund (FWF)
SFB project SpyCoDe 10.55776/F85, by the FWF projects ZK-35 and W1255-N23, and by
the ERC Advanced Grant VAMOS 101020093. Open access funding provided by Institute
of Science and Technology (IST Austria).
article_number: '43'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana
full_name: Oliveira da Costa, Ana
id: f347ec37-6676-11ee-b395-a888cb7b4fb4
last_name: Oliveira da Costa
orcid: 0000-0002-8741-5799
citation:
ama: Bartocci E, Chalupa M, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode
automata. Acta Informatica. 2025;62(4). doi:10.1007/s00236-025-00509-8
apa: Bartocci, E., Chalupa, M., Henzinger, T. A., Nickovic, D., & Oliveira da
Costa, A. (2025). Hypernode automata. Acta Informatica. Springer Nature.
https://doi.org/10.1007/s00236-025-00509-8
chicago: Bartocci, Ezio, Marek Chalupa, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira da Costa. “Hypernode Automata.” Acta Informatica. Springer
Nature, 2025. https://doi.org/10.1007/s00236-025-00509-8.
ieee: E. Bartocci, M. Chalupa, T. A. Henzinger, D. Nickovic, and A. Oliveira da
Costa, “Hypernode automata,” Acta Informatica, vol. 62, no. 4. Springer
Nature, 2025.
ista: Bartocci E, Chalupa M, Henzinger TA, Nickovic D, Oliveira da Costa A. 2025.
Hypernode automata. Acta Informatica. 62(4), 43.
mla: Bartocci, Ezio, et al. “Hypernode Automata.” Acta Informatica, vol.
62, no. 4, 43, Springer Nature, 2025, doi:10.1007/s00236-025-00509-8.
short: E. Bartocci, M. Chalupa, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa,
Acta Informatica 62 (2025).
corr_author: '1'
date_created: 2025-12-29T12:07:12Z
date_published: 2025-12-09T00:00:00Z
date_updated: 2026-01-05T12:27:41Z
day: '09'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s00236-025-00509-8
ec_funded: 1
external_id:
arxiv:
- '2305.02836'
file:
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checksum: 06ed45a1218ad8464818803ae2968aaf
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date_created: 2026-01-05T12:26:43Z
date_updated: 2026-01-05T12:26:43Z
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file_name: 2025_ActaInformatica_Bartocci.pdf
file_size: 7117003
relation: main_file
success: 1
file_date_updated: 2026-01-05T12:26:43Z
has_accepted_license: '1'
intvolume: ' 62'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e
grant_number: F8502
name: Interface Theory for Security and Privacy
publication: Acta Informatica
publication_identifier:
eissn:
- 1432-0525
issn:
- 0001-5903
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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- id: '14405'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Hypernode automata
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: 62
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20867'
abstract:
- lang: eng
text: We discuss the embeddability of subspaces of the Gromov–Hausdorff space, which
consists of isometry classes of compact metric spaces endowed with the Gromov–Hausdorff
distance, into Hilbert spaces. These embeddings are particularly valuable for
applications to topological data analysis. We prove that its subspace consisting
of metric spaces with at most n points has asymptotic dimension n(n−1)∕2. Thus,
there exists a coarse embedding of that space into a Hilbert space. On the contrary,
if the number of points is not bounded, then the subspace cannot be coarsely embedded
into any uniformly convex Banach space and so, in particular, into any Hilbert
space. Furthermore, we prove that, even if we restrict to finite metric spaces
whose diameter is bounded by some constant, the subspace still cannot be bi-Lipschitz
embedded into any finite-dimensional Hilbert space. We obtain both nonembeddability
results by finding obstructions to coarse and bi-Lipschitz embeddings in families
of isometry classes of finite subsets of the real line endowed with the Euclidean–Hausdorff
distance.
acknowledgement: "The author was supported by the FWF Grant, Project number I4245-N35.
The author would like to thank Thomas Weighill for the helpful discussions around
Theorem 3.10, and Takamitsu Yamauchi for bringing to my attention the fundamental
reference [35]. Furthermore, the author\r\nis thankful for the detailed and helpful
comments of the reviewer of this manuscript."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
citation:
ama: Zava N. Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff
space into Hilbert spaces. Algebraic & Geometric Topology. 2025;25(8):5153-5174.
doi:10.2140/agt.2025.25.5153
apa: Zava, N. (2025). Coarse and bi-Lipschitz embeddability of subspaces of the
Gromov–Hausdorff space into Hilbert spaces. Algebraic & Geometric Topology.
Mathematical Sciences Publishers. https://doi.org/10.2140/agt.2025.25.5153
chicago: Zava, Nicolò. “Coarse and Bi-Lipschitz Embeddability of Subspaces of the
Gromov–Hausdorff Space into Hilbert Spaces.” Algebraic & Geometric Topology.
Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/agt.2025.25.5153.
ieee: N. Zava, “Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff
space into Hilbert spaces,” Algebraic & Geometric Topology, vol. 25,
no. 8. Mathematical Sciences Publishers, pp. 5153–5174, 2025.
ista: Zava N. 2025. Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff
space into Hilbert spaces. Algebraic & Geometric Topology. 25(8), 5153–5174.
mla: Zava, Nicolò. “Coarse and Bi-Lipschitz Embeddability of Subspaces of the Gromov–Hausdorff
Space into Hilbert Spaces.” Algebraic & Geometric Topology, vol. 25,
no. 8, Mathematical Sciences Publishers, 2025, pp. 5153–74, doi:10.2140/agt.2025.25.5153.
short: N. Zava, Algebraic & Geometric Topology 25 (2025) 5153–5174.
corr_author: '1'
date_created: 2025-12-29T12:09:09Z
date_published: 2025-11-20T00:00:00Z
date_updated: 2026-01-05T12:19:09Z
day: '20'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.2140/agt.2025.25.5153
external_id:
arxiv:
- '2303.04730'
file:
- access_level: open_access
checksum: 1e05b4f17a44500ae1ae1e21bc636f6a
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T12:16:38Z
date_updated: 2026-01-05T12:16:38Z
file_id: '20943'
file_name: 2025_AlgebraicGeomTopology_Zava.pdf
file_size: 574389
relation: main_file
success: 1
file_date_updated: 2026-01-05T12:16:38Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 5153-5174
project:
- _id: 26AD5D90-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04245
name: Algebraic Footprints of Geometric Features in Homology
publication: Algebraic & Geometric Topology
publication_identifier:
eissn:
- 1472-2739
issn:
- 1472-2747
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff
space into Hilbert spaces
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: 25
year: '2025'
...
---
OA_place: repository
OA_type: hybrid
_id: '20883'
abstract:
- lang: eng
text: 'Evading imminent predator threat is critical for survival. Effective defensive
strategies can vary, even between closely related species. However, the neural
basis of such species-specific behaviours is still poorly understood. Here we
find that two sister species of deer mice (genus Peromyscus) show different responses
to the same looming stimulus: P. maniculatus, which occupies densely vegetated
habitats, predominantly escapes, while the open field specialist, P. polionotus,
briefly freezes. This difference arises from species-specific escape thresholds,
is largely context-independent, and can be triggered by both visual and auditory
threat stimuli. Using immunohistochemistry and electrophysiological recordings,
we find that although visual threat activates the superior colliculus in both
species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour
differs. While dPAG activity scales with running speed in P. maniculatus, neural
activity in the dPAG of P. polionotus correlates poorly with movement, including
during visually triggered escape. Moreover, optogenetic activation of dPAG neurons
elicits acceleration in P. maniculatus but not P. polionotus, while their chemogenetic
inhibition during a looming stimulus delays escape onset in P. maniculatus to
match that of P. polionotus. Together, we trace species-specific escape thresholds
to a central circuit node, downstream of peripheral sensory neurons, localizing
an ecologically relevant behavioural difference to a specific region of the mammalian
brain.'
article_processing_charge: No
author:
- first_name: Baier
full_name: Felix, Baier
last_name: Felix
- first_name: Katja
full_name: Reinhard, Katja
last_name: Reinhard
- first_name: Bram
full_name: Nuttin, Bram
last_name: Nuttin
- first_name: Arnau
full_name: Sans Dublanc, Arnau
last_name: Sans Dublanc
- first_name: Chen
full_name: Liu, Chen
last_name: Liu
- first_name: Victoria
full_name: Tong, Victoria
last_name: Tong
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
- first_name: Keimpe
full_name: Wierda, Keimpe
last_name: Wierda
- first_name: Karl
full_name: Farrow, Karl
last_name: Farrow
- first_name: Hopi
full_name: Hoekstra, Hopi
last_name: Hoekstra
citation:
ama: Felix B, Reinhard K, Nuttin B, et al. The neural basis of species-specific
defensive behaviour in Peromyscus mice. 2025. doi:10.5061/DRYAD.Q2BVQ83XC
apa: Felix, B., Reinhard, K., Nuttin, B., Sans Dublanc, A., Liu, C., Tong, V., …
Hoekstra, H. (2025). The neural basis of species-specific defensive behaviour
in Peromyscus mice. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83XC
chicago: Felix, Baier, Katja Reinhard, Bram Nuttin, Arnau Sans Dublanc, Chen Liu,
Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi Hoekstra.
“The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.”
Dryad, 2025. https://doi.org/10.5061/DRYAD.Q2BVQ83XC.
ieee: B. Felix et al., “The neural basis of species-specific defensive behaviour
in Peromyscus mice.” Dryad, 2025.
ista: Felix B, Reinhard K, Nuttin B, Sans Dublanc A, Liu C, Tong V, Murmann JS,
Wierda K, Farrow K, Hoekstra H. 2025. The neural basis of species-specific defensive
behaviour in Peromyscus mice, Dryad, 10.5061/DRYAD.Q2BVQ83XC.
mla: Felix, Baier, et al. The Neural Basis of Species-Specific Defensive Behaviour
in Peromyscus Mice. Dryad, 2025, doi:10.5061/DRYAD.Q2BVQ83XC.
short: B. Felix, K. Reinhard, B. Nuttin, A. Sans Dublanc, C. Liu, V. Tong, J.S.
Murmann, K. Wierda, K. Farrow, H. Hoekstra, (2025).
date_created: 2025-12-30T07:36:29Z
date_published: 2025-06-23T00:00:00Z
date_updated: 2026-01-05T11:38:41Z
day: '23'
department:
- _id: GradSch
doi: 10.5061/DRYAD.Q2BVQ83XC
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.q2bvq83xc
month: '06'
oa: 1
oa_version: Submitted Version
publisher: Dryad
related_material:
record:
- id: '20101'
relation: used_in_publication
status: public
status: public
title: The neural basis of species-specific defensive behaviour in Peromyscus mice
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '20920'
abstract:
- lang: eng
text: "Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18)
are functions that require a prescribed number of sequential steps T to evaluate,
yet their output can be verified in time much faster than T. Since their introduction,
VDFs have gained a lot of attention due to their applications in blockchain protocols,
randomness beacons, timestamping and deniability. This thesis explores the theory
and applications of VDFs, focusing on enhancing their soundness, efficiency and
practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated
squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe
iterated squaring assumption states that, for a random group element x, the result
of VDF cannot be computed significantly faster than performing T sequential squarings
if the group order is unknown. To make the result verifiable a prover can compute
a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified
in time much less than T.\r\n\r\nWe first present new constructions of statistically
sound proofs of exponentiation, which are an important building block in the construction
of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness
means that the proofs remain secure against computationally unbounded adversaries,
in particular, it remains secure even when the group order is known. We thereby
address limitations in previous PoE protocols which either required (non-standard)
hardness assumptions or a lot of parallel repetitions. Our construction significantly
reduces the proof size of statistically sound PoEs that allow for a structured
exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly,
we introduce improved batching techniques for PoEs, which allow multiple proofs
to be aggregated and verified with minimal overhead. These protocols optimize
communication and computation complexity in large-scale blockchain environments
and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe
then construct VDFs with enhanced properties such as zero-knowledge and watermarkability.
It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable
new cryptographic primitives called short-lived proofs and signatures. The validity
of such proofs and signatures expires after a predefined amount of time T, i.e.,
they are deniable after time T. Our constructions improve upon the constructions
by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably
weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing,
providing cryptographically sound proofs of non-primality for large Proth numbers.
This work gives a surprising application of VDFs in the area of computational
number theory.\r\n\r\nTogether, our contributions advance both the theoretical
foundations and the real-world usability of VDFs in general and in particular
of PoEs, making them more adaptable and secure for current and emerging cryptographic
applications."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Charlotte
full_name: Hoffmann, Charlotte
id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7
last_name: Hoffmann
orcid: 0000-0003-2027-5549
citation:
ama: Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:10.15479/AT-ISTA-20920
apa: Hoffmann, C. (2025). Theory and applications of verifiable delay functions.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20920
chicago: Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20920.
ieee: C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute
of Science and Technology Austria, 2025.
ista: Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute
of Science and Technology Austria.
mla: Hoffmann, Charlotte. Theory and Applications of Verifiable Delay Functions.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20920.
short: C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute
of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2026-01-02T10:46:47Z
date_published: 2025-12-31T00:00:00Z
date_updated: 2026-04-16T09:11:08Z
day: '31'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/AT-ISTA-20920
file:
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checksum: 8a099fbf54963bd0be38f7ce73658682
content_type: application/x-zip-compressed
creator: choffman
date_created: 2026-01-02T10:39:16Z
date_updated: 2026-01-02T10:39:16Z
file_id: '20921'
file_name: 2025_Hoffmann_Charlotte_Source.zip
file_size: 8355494
relation: source_file
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checksum: 9521c07bfb2bb5b14a49c09fcfc96474
content_type: application/pdf
creator: choffman
date_created: 2026-01-02T10:39:26Z
date_updated: 2026-01-02T10:39:26Z
file_id: '20922'
file_name: 2025_Hoffmann_Charlotte_Thesis.pdf
file_size: 2258804
relation: main_file
success: 1
file_date_updated: 2026-01-02T10:39:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '116'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13143'
relation: part_of_dissertation
status: public
- id: '20701'
relation: part_of_dissertation
status: public
- id: '12176'
relation: part_of_dissertation
status: public
- id: '20556'
relation: earlier_version
status: public
- id: '19778'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Theory and applications of verifiable delay functions
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20924'
abstract:
- lang: eng
text: "Pioneer transcription factors (TFs) possess the ability to read out DNA motifs
embedded within nucleosomes, driving changes in gene expression during cellular
differentiation and reprogramming. Here, we present selected engagement on nucleosome
sequencing (SeEN-seq), a protocol designed to systematically identify potential
TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly,
SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This
protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes
for cryo-EM structure determination using single-particle analysis.\r\nFor complete
details on the use and execution of this protocol, please refer to Michael et
al.1"
acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the
NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department
of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded
by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max
Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).
article_number: '104295'
article_processing_charge: Yes
article_type: original
author:
- first_name: Wataru
full_name: Kobayashi, Wataru
last_name: Kobayashi
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Siwat
full_name: Ruangroengkulrith, Siwat
last_name: Ruangroengkulrith
- first_name: Maximilian
full_name: Kümmecke, Maximilian
last_name: Kümmecke
- first_name: Kikuë
full_name: Tachibana, Kikuë
last_name: Tachibana
citation:
ama: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol
for integrative analysis of transcription factor-nucleosome interactions using
SeEN-seq and cryo-EM structure determination. STAR Protocols. 2025;7. doi:10.1016/j.xpro.2025.104295
apa: Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., & Tachibana,
K. (2025). Protocol for integrative analysis of transcription factor-nucleosome
interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols.
Elsevier. https://doi.org/10.1016/j.xpro.2025.104295
chicago: Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian
Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription
Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
STAR Protocols. Elsevier, 2025. https://doi.org/10.1016/j.xpro.2025.104295.
ieee: W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana,
“Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination,” STAR Protocols, vol.
7. Elsevier, 2025.
ista: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025.
Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295.
mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription
Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
STAR Protocols, vol. 7, 104295, Elsevier, 2025, doi:10.1016/j.xpro.2025.104295.
short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana,
STAR Protocols 7 (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-26T00:00:00Z
date_updated: 2026-06-18T18:27:57Z
day: '26'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.xpro.2025.104295
external_id:
pmid:
- '41455105'
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.xpro.2025.104295
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9136c684-16d5-11f0-9cad-91c0177b365f
grant_number: '101162145'
name: Circadian structural transitions of chromatin
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination
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: 7
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20925'
abstract:
- lang: eng
text: 'We prove normal typicality and dynamical typicality for a (centered) random
block-band matrix model with block-dependent variances. A key feature of our model
is that we achieve intermediate equilibration times, an aspect that has not been
proven rigorously in any model before. Our proof builds on recently established
concentration estimates for products of resolvents of Wigner type random matrices
(Erdős and Riabov in Commun Math Phys 405(12): 282, 2024) and an intricate analysis
of the deterministic approximation.'
acknowledgement: L.E. and J.H. are supported by the ERC Advanced Grant “RMTBeyond”
No. 101020331. Moreover, J.H. acknowledges (partial) financial support by the ERC
Consolidator Grant “ProbQuant” (jointly with the Swiss State Secretariat for Education,
Research and Innovation). C.V. was (partially) supported by the German Academic
Scholarship Foundation and the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) – TRR 352 – Project-ID 470903074. Moreover, C.V. acknowledges (partial)
financial support by the ERC Starting Grant “FermiMath" No. 101040991 and the ERC
Consolidator Grant “RAMBAS” No. 10104424, funded by the European Union. Open access
funding provided by Institute of Science and Technology (IST Austria).
article_number: '5'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Cornelia
full_name: Vogel, Cornelia
id: 1cd0554a-ea28-11f0-9f40-ff76440883cd
last_name: Vogel
citation:
ama: Erdös L, Henheik SJ, Vogel C. Normal typicality and dynamical typicality for
a random block-band matrix model. Letters in Mathematical Physics. 2025;116.
doi:10.1007/s11005-025-02037-5
apa: Erdös, L., Henheik, S. J., & Vogel, C. (2025). Normal typicality and dynamical
typicality for a random block-band matrix model. Letters in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s11005-025-02037-5
chicago: Erdös, László, Sven Joscha Henheik, and Cornelia Vogel. “Normal Typicality
and Dynamical Typicality for a Random Block-Band Matrix Model.” Letters in
Mathematical Physics. Springer Nature, 2025. https://doi.org/10.1007/s11005-025-02037-5.
ieee: L. Erdös, S. J. Henheik, and C. Vogel, “Normal typicality and dynamical typicality
for a random block-band matrix model,” Letters in Mathematical Physics,
vol. 116. Springer Nature, 2025.
ista: Erdös L, Henheik SJ, Vogel C. 2025. Normal typicality and dynamical typicality
for a random block-band matrix model. Letters in Mathematical Physics. 116, 5.
mla: Erdös, László, et al. “Normal Typicality and Dynamical Typicality for a Random
Block-Band Matrix Model.” Letters in Mathematical Physics, vol. 116, 5,
Springer Nature, 2025, doi:10.1007/s11005-025-02037-5.
short: L. Erdös, S.J. Henheik, C. Vogel, Letters in Mathematical Physics 116 (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-26T00:00:00Z
date_updated: 2026-01-05T11:22:25Z
day: '26'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s11005-025-02037-5
ec_funded: 1
external_id:
pmid:
- '41459414'
has_accepted_license: '1'
intvolume: ' 116'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s11005-025-02037-5
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- 1573-0530
issn:
- 0377-9017
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Normal typicality and dynamical typicality for a random block-band matrix model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20926'
abstract:
- lang: eng
text: Most current machine learning interatomic potentials (MLIPs) rely on short-range
approximations, without explicit treatment of long-range electrostatics. To address
this, we recently developed the Latent Ewald Summation (LES) method, which infers
electrostatic interactions, polarization, and Born effective charges (BECs), just
by learning from energy and force training data. Here, we present LES as a standalone
library, compatible with any short-range MLIP, and demonstrate its integration
with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark
LES-enhanced models on distinct systems, including bulk water, polar dipeptides,
and gold dimer adsorption on defective substrates, and show that LES not only
captures correct electrostatics but also improves accuracy. Additionally, we scale
LES to large and chemically diverse data by training MACELES-OFF on the SPICE
set containing molecules and clusters, making a universal MLIP with electrostatics
for organic systems, including biomolecules. MACELES-OFF is more accurate than
its short-range counterpart (MACE-OFF) trained on the same data set, predicts
dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling
efficient long-range electrostatics without directly training on electrical properties,
LES paves the way for electrostatic foundation MLIPs.
acknowledgement: Research reported in this publication was supported by the National
Institute Of General Medical Sciences of the National Institutes of Health under
Award Number R35GM159986. The content is solely the responsibility of the authors
and does not necessarily represent the official views of the National Institutes
of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis
Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP
Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific
Computing Center (NERSC), a Department of Energy Office of Science User Facility
using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for
valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating
discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Xiaoyu
full_name: Wang, Xiaoyu
id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
last_name: Wang
- first_name: Santiago
full_name: Vargas, Santiago
last_name: Vargas
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Theo Jaffrelot
full_name: Inizan, Theo Jaffrelot
last_name: Inizan
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range
electrostatics in machine learning interatomic potentials. Journal of Chemical
Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400
apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., &
Cheng, B. (2025). A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials. Journal of Chemical Theory and
Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400
chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King,
Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework
for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal
of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400.
ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials,” Journal of Chemical Theory and
Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724,
2025.
ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal
augmentation framework for long-range electrostatics in machine learning interatomic
potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724.
mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics
in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and
Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24,
doi:10.1021/acs.jctc.5c01400.
short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal
of Chemical Theory and Computation 21 (2025) 12709–12724.
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-10T00:00:00Z
date_updated: 2026-01-05T11:34:21Z
day: '10'
department:
- _id: GradSch
- _id: BiCh
doi: 10.1021/acs.jctc.5c01400
external_id:
arxiv:
- '2507.14302'
pmid:
- '41368735 '
intvolume: ' 21'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.14302
month: '12'
oa: 1
oa_version: Preprint
page: 12709-12724
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A universal augmentation framework for long-range electrostatics in machine
learning interatomic potentials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20927'
abstract:
- lang: eng
text: Cavity-magnon polaritons are hybrid excitations from the interaction between
cavity photons and magnons, the quanta of collective spin oscillations. Along
with the tunability of the magnon-photon coupling strength, fast information transfer
and conversion speed are desired in hybrid devices. This can be achieved utilizing
the propagating nature of spin waves with nonzero momentum for their ultrafast
time dynamics and reduced ohmic dissipation. Antiferromagnets are particularly
interesting as hosts for magnons since stray-field interactions are minimized
and they support multiple modes with distinctive magnetic-field behavior across
the phase diagram. Chromium trichloride (CrCl3) is a van der Waals layered antiferromagnet
having a strong easy-plane anisotropy and a weak in-plane easy-axis anisotropy.
Despite some magnetic resonance studies, the impact of magnetic reorientation
of spins in CrCl3 on the cavity-magnon-polariton interaction strength as a function
of magnetic field remains largely unexplored. In this study, we investigate the
coupling between magnons in CrCl3 and photons in a coplanar waveguide resonator
as a function of magnetic field. In particular, we find that the magnon-photon
coupling strength varies nonmonotonically and distinctly with the magnetic field
for the acoustic and the optical magnons, which can be utilized to tune the magnon-photon
coupling strength using an external magnetic field as a knob. We find the signature
of spin-flop transition in the two harmonics of the cavity due to a stronger dispersive
coupling between optical magnons and cavity photons at lower fields. Additionally,
we find standing modes formed by spin waves with nonzero momentum associated with
the two hybrid magnons when the external field is applied at an angle with the
crystal plane. These modes do not undergo substantial coupling with the cavity
mode unlike the antiferromagnetic modes and can be used as low-loss propagation
channels in hybrid devices.
acknowledgement: We thank R. Vijayaraghavan, V. Singh, A. Kamra, A. Barman, M. Patankar,
S. Kundu, S. Hazra, S. Sahu, A. Riswadkar, A. Bhattacharjee, and S. Das for helpful
discussions and experimental assistance. We acknowledge the Swarnajayanti Fellowship
of the Department of Science and Technology (for M.M.D.), DST Nanomission Grant
No. SR/NM/NS-45/2016, SERB SUPRA Grant No. SPR/2019/001247, ONRG Grant No. N62909–18-1–2058,
and the Department of Atomic Energy of the Government of India Grant No. 12-R&D-TFR5.10–0100
for support.
article_number: '214443'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Supriya
full_name: Mandal, Supriya
last_name: Mandal
- first_name: Krishnendu
full_name: Maji, Krishnendu
id: 76bc9e9f-ba0b-11ee-8184-90edabd17a58
last_name: Maji
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Souvik
full_name: Sasmal, Souvik
last_name: Sasmal
- first_name: Soham
full_name: Manni, Soham
last_name: Manni
- first_name: John
full_name: Jesudasan, John
last_name: Jesudasan
- first_name: Pratap
full_name: Raychaudhuri, Pratap
last_name: Raychaudhuri
- first_name: Arumugam
full_name: Thamizhavel, Arumugam
last_name: Thamizhavel
- first_name: Mandar M.
full_name: Deshmukh, Mandar M.
last_name: Deshmukh
citation:
ama: Mandal S, Maji K, Kapoor L, et al. Cavity based sensing of antiferromagnetic
canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton
system. Physical Review B. 2025;112(21). doi:10.1103/bdd1-b8ys
apa: Mandal, S., Maji, K., Kapoor, L., Sasmal, S., Manni, S., Jesudasan, J., … Deshmukh,
M. M. (2025). Cavity based sensing of antiferromagnetic canting and nonzero-momentum
spin waves in a van der Waals cavity-magnon-polariton system. Physical Review
B. American Physical Society. https://doi.org/10.1103/bdd1-b8ys
chicago: Mandal, Supriya, Krishnendu Maji, Lucky Kapoor, Souvik Sasmal, Soham Manni,
John Jesudasan, Pratap Raychaudhuri, Arumugam Thamizhavel, and Mandar M. Deshmukh.
“Cavity Based Sensing of Antiferromagnetic Canting and Nonzero-Momentum Spin Waves
in a van Der Waals Cavity-Magnon-Polariton System.” Physical Review B.
American Physical Society, 2025. https://doi.org/10.1103/bdd1-b8ys.
ieee: S. Mandal et al., “Cavity based sensing of antiferromagnetic canting
and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system,”
Physical Review B, vol. 112, no. 21. American Physical Society, 2025.
ista: Mandal S, Maji K, Kapoor L, Sasmal S, Manni S, Jesudasan J, Raychaudhuri P,
Thamizhavel A, Deshmukh MM. 2025. Cavity based sensing of antiferromagnetic canting
and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system.
Physical Review B. 112(21), 214443.
mla: Mandal, Supriya, et al. “Cavity Based Sensing of Antiferromagnetic Canting
and Nonzero-Momentum Spin Waves in a van Der Waals Cavity-Magnon-Polariton System.”
Physical Review B, vol. 112, no. 21, 214443, American Physical Society,
2025, doi:10.1103/bdd1-b8ys.
short: S. Mandal, K. Maji, L. Kapoor, S. Sasmal, S. Manni, J. Jesudasan, P. Raychaudhuri,
A. Thamizhavel, M.M. Deshmukh, Physical Review B 112 (2025).
date_created: 2026-01-04T23:01:34Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-01-05T10:07:04Z
day: '19'
department:
- _id: MaIb
- _id: JoFi
doi: 10.1103/bdd1-b8ys
external_id:
arxiv:
- '2512.05236'
intvolume: ' 112'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2512.05236
month: '12'
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'
related_material:
record:
- id: '20940'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin
waves in a van der Waals cavity-magnon-polariton system
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2025'
...
---
APC_amount: 7068 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20929'
abstract:
- lang: eng
text: Insulin/insulin-like growth factor signaling inhibits FOXO transcription factors
to control development, homeostasis, and aging. Here, we use proximity labeling
to identify proteins interacting with the C. elegans FOXO DAF-16. We show that
in well-fed, unstressed animals harboring active insulin signaling, DAF-16 forms
a complex with the PAR-1/MARK serine/threonine kinase, a key regulator of cell
polarity. PAR-1 inhibits DAF-16 accumulation and promotes DAF-16 phosphorylation
at S249, at a conserved motif that PAR-1/human MARK2 phosphorylates in vitro.
DAF-2 insulin-like receptor signaling stimulates DAF-16 S249 phosphorylation,
suggesting DAF-2 activates PAR-1. DAF-2 also promotes PAR-1 expression by inhibiting
DAF-16. PAR-1 knockdown, or DAF-16 S249A, prolong lifespan, whereas phosphomimetic
DAF-16 S249D suppresses the longevity of daf-2 mutants. At low insulin signaling,
DAF-16 proximity labeling highlights transcription factors, chromatin regulators,
and DNA repair proteins. One interactor, the zinc finger/homeobox protein ZFH-2/ZFHX3,
forms a complex with DAF-16 and prolongs lifespan. Our work provides entry points
for hypothesis-driven studies of FOXO function and longevity.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank de Bono lab members for helpful comments on the manuscript,
and the Mass Spec Facility at the Max Perutz Labs, notably WeiQiang Chen and Markus
Hartl, for invaluable discussions and comments on mass spec analyses of worm samples.
All LC-MS/MS analyses were performed on instruments of the Vienna BioCenter Core
Facilities (VBCF). Microscopy was supported by the Scientific Services Units (SSU)
of ISTA through resources provided by the Imaging & Optics Facility (IOF). We are
grateful to Dr. Geraldine Seydoux (Johns Hopkins University) for worm strains and
plasmids, and Dr. Seung-Jae V. Lee (KAIST) for RNAi clones. We are grateful to Ekaterina
Lashmanova for designing the daf-16::TbID::mNG::3xFLAG knock-in construct and for
her outstanding support in the lab. This work was supported by a Wellcome Investigator
Award (209504/A/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie
agreement No 754411).
article_number: '11355'
article_processing_charge: Yes
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Hanna
full_name: Schön, Hanna
id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425
last_name: Schön
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Artan M, Schön H, de Bono M. Proximity labeling of DAF-16 FOXO highlights aging
regulatory proteins. Nature Communications. 2025;16. doi:10.1038/s41467-025-66409-0
apa: Artan, M., Schön, H., & de Bono, M. (2025). Proximity labeling of DAF-16
FOXO highlights aging regulatory proteins. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-025-66409-0
chicago: Artan, Murat, Hanna Schön, and Mario de Bono. “Proximity Labeling of DAF-16
FOXO Highlights Aging Regulatory Proteins.” Nature Communications. Springer
Nature, 2025. https://doi.org/10.1038/s41467-025-66409-0.
ieee: M. Artan, H. Schön, and M. de Bono, “Proximity labeling of DAF-16 FOXO highlights
aging regulatory proteins,” Nature Communications, vol. 16. Springer Nature,
2025.
ista: Artan M, Schön H, de Bono M. 2025. Proximity labeling of DAF-16 FOXO highlights
aging regulatory proteins. Nature Communications. 16, 11355.
mla: Artan, Murat, et al. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory
Proteins.” Nature Communications, vol. 16, 11355, Springer Nature, 2025,
doi:10.1038/s41467-025-66409-0.
short: M. Artan, H. Schön, M. de Bono, Nature Communications 16 (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:34Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2026-05-20T08:10:18Z
day: '11'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1038/s41467-025-66409-0
ec_funded: 1
external_id:
pmid:
- '41381452'
file:
- access_level: open_access
checksum: 748e2e003b878b85b6048d51621d6aae
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T10:58:28Z
date_updated: 2026-01-05T10:58:28Z
file_id: '20941'
file_name: 2025_NatureComm_Artan.pdf
file_size: 1642352
relation: main_file
success: 1
file_date_updated: 2026-01-05T10:58:28Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins
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: 16
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20930'
abstract:
- lang: eng
text: "Context. Beta Pictoris is an A-type star that hosts a complex planetary system
with two massive gas giants and a prominent debris disc. Variable absorption lines
in its stellar spectrum have been interpreted as signatures of exocomets – comet-like
bodies transiting the star. Stellar flybys can gravitationally perturb objects
in the outer comet reservoir, altering their orbits and potentially injecting
them into the inner system, thereby triggering exocomet showers.\r\nAims. We assessed
the contribution of stellar flybys to the observed exocomet activity by reconstructing
the stellar encounter history of β Pictoris in the past and future.\r\nMethods.
We used Gaia DR3 data, supplemented with radial velocities from complementary
spectroscopic surveys, to compile a catalogue of stars currently within 80 pc
of β Pictoris. Their orbits were integrated backwards and forwards in time in
an axisymmetric Galactic potential (via the GALA package) to identify encounters
within 2 pc of the system.\r\nResults. We identified 99 416 stars currently within
80 pc of β Pictoris with resolved kinematics. Among these, 49 stars (including
the eight components of five binaries) encounter β Pictoris within 2 pc between
–1.5 Myr and +2 Myr. For four of the binaries, the centre-of-mass trajectories
also pass within 2 pc. We estimated the sample to be more than 60% complete within
0.5 Myr of today.\r\nConclusions. Despite β Pictoris being the eponym of its famous
moving group, none of the identified encounters involved its moving group members;
all are unrelated field stars. We found no encounter capable of shaping the observed
disc structures, although stellar flybys may contribute to the long-term evolution
of an Oort Cloud-like structure. Our catalogue constitutes the most complete reconstruction
of the β Pictoris encounter history to date and provides a robust foundation for
future dynamical simulations."
acknowledgement: We thank the referee for their suggestions and comments, which helped
us improve the quality and clarity of the paper. JLGM and EV acknowledge the support
from the Spanish Ministry of Science and Innovation/State Agency of Research (MCIN/AEI)
under the grant PID2021-127289-NB-I00. ST acknowledges the funding from the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
grant agreement No. 101034413. AJM acknowledges support from the Swedish National
Space Agency (Career Grant 2023-00146) and from the Swedish Research Council (Project
Grant 2022-04043). JLGM also sincerely thanks AMP for his careful final reading
of this manuscript. This 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). Funding for the DPAC has been provided
by national institutions, in particular the institutions participating in the Gaia
Multilateral Agreement. We acknowledge the use of the public data products from
RAVE (https://www.rave-survey.org), GALAH (https://galah-survey.org), APOGEE ((https://www.sdss.org)
and LAMOST (http://www.lamost.org) surveys. This research has also made use of the
SIMBAD database and the VizieR catalogue access tool, operated at CDS, Strasbourg,
France, as well as the NASA Astrophysics Data System Bibliographic Services and
the arXiv pre-print server operated by Cornell University. Computational analyses
in this work relied extensively on the NumPy and SciPy libraries for numerical computing,
matplotlib and seaborn for data visualization, and the Gala package for Galactic
dynamics. This work also made use of Astropy, a community-developed core PYTHON
package and an ecosystem of tools and resources for astronomy. We thank the developers
and maintainers of these open-source resources for their invaluable contributions
to the astronomical community.
article_number: A237
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J. L.
full_name: Gragera-Más, J. L.
last_name: Gragera-Más
- first_name: Santiago
full_name: Torres Rodriguez, Santiago
id: a8df4360-4328-11ee-8f1a-e502d0c83fc2
last_name: Torres Rodriguez
orcid: 0000-0002-3150-8988
- first_name: A. J.
full_name: Mustill, A. J.
last_name: Mustill
- first_name: E.
full_name: Villaver, E.
last_name: Villaver
citation:
ama: Gragera-Más JL, Torres Rodriguez S, Mustill AJ, Villaver E. A kinematic history
of stellar encounters with Beta Pictoris. Astronomy & Astrophysics.
2025;704. doi:10.1051/0004-6361/202555940
apa: Gragera-Más, J. L., Torres Rodriguez, S., Mustill, A. J., & Villaver, E.
(2025). A kinematic history of stellar encounters with Beta Pictoris. Astronomy
& Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202555940
chicago: Gragera-Más, J. L., Santiago Torres Rodriguez, A. J. Mustill, and E. Villaver.
“A Kinematic History of Stellar Encounters with Beta Pictoris.” Astronomy &
Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202555940.
ieee: J. L. Gragera-Más, S. Torres Rodriguez, A. J. Mustill, and E. Villaver, “A
kinematic history of stellar encounters with Beta Pictoris,” Astronomy &
Astrophysics, vol. 704. EDP Sciences, 2025.
ista: Gragera-Más JL, Torres Rodriguez S, Mustill AJ, Villaver E. 2025. A kinematic
history of stellar encounters with Beta Pictoris. Astronomy & Astrophysics.
704, A237.
mla: Gragera-Más, J. L., et al. “A Kinematic History of Stellar Encounters with
Beta Pictoris.” Astronomy & Astrophysics, vol. 704, A237, EDP Sciences,
2025, doi:10.1051/0004-6361/202555940.
short: J.L. Gragera-Más, S. Torres Rodriguez, A.J. Mustill, E. Villaver, Astronomy
& Astrophysics 704 (2025).
date_created: 2026-01-04T23:01:34Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-02-16T12:15:07Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202555940
ec_funded: 1
external_id:
arxiv:
- '2510.02509'
file:
- access_level: open_access
checksum: 2fb4d5a1603043aa7931a31f2c180877
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T11:06:16Z
date_updated: 2026-01-05T11:06:16Z
file_id: '20942'
file_name: 2025_AstronomyAstrophysics_GrageraMas.pdf
file_size: 11021467
relation: main_file
success: 1
file_date_updated: 2026-01-05T11:06:16Z
has_accepted_license: '1'
intvolume: ' 704'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: A kinematic history of stellar encounters with Beta Pictoris
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: 704
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20931'
abstract:
- lang: eng
text: "Context. Asymmetries in the observed rotational splittings of a multiplet
contain information about the star’s rotation profile and internal magnetic field.
Moreover, the frequency regularities of multiplets can be used for mode identification.
However, to exploit this information, highly accurate theoretical predictions
are needed.\r\n\r\nAims. We aim to quantify the difference in the predicted mode
asymmetries between a 1D perturbative method and a 2D method that includes a 2D
stellar structure model, which takes rotation into account. We then place these
differences between 1D and 2D methods in the context of asteroseismic measurements
of internal magnetic fields. We only focus on the asymmetries and not on possible
additional frequency peaks that can arise when the magnetic and rotation axis
are misaligned.\r\n\r\nMethods. We coupled the 1D pulsation codes GYRE and StORM
to the 2D stellar structure code ESTER and compared the oscillation predictions
with the results from the 2D TOP pulsation code. We focused on zero-age main-sequence
models representative of rotating β Cephei pulsators spinning at up to 20 per
cent of the critical Keplerian rotation rate. Specifically, we investigated low-radial-order
gravity and pressure modes.\r\n\r\nResults. We find a generally good agreement
between the oscillation frequencies resulting from the 1D and 2D pulsation codes.
We report differences in predicted mode multiplet asymmetries of mostly below
0.06 d−1. Since the magnetic asymmetries are small compared to the differences
in the rotational asymmetries resulting from the 1D and 2D predictions, accurate
measurements of the magnetic field are in most cases challenging.\r\n\r\nConclusions.
Differences in the predicted mode asymmetries of a rotating star between 1D perturbative
methods and 2D non-perturbative methods can greatly hinder accurate measurements
of internal magnetic fields in main-sequence pulsators with low-order modes. Nevertheless,
reasonably accurate measurements could be possible with npg ≥ 2 modes if the internal
rotation is roughly below 10 per cent of the Keplerian critical rotation frequency
for (aligned) magnetic fields of the order of a few hundred kilogauss. While the
differences between the 1D and 2D frequency predictions are mostly too large for
internal magnetic field detections, the rotational asymmetries predicted by StORM
are in general accurate enough for asteroseismic modelling of the stellar rotation
in main-sequence stars with identified low-order modes."
acknowledgement: 'We thank the anonymous referee for their comments on the manuscript,
Dario Fritzewski for providing the distribution of fractions of critical rotation
for the β Cephei sample, and Zhao Guo for the discussions. The research leading
to these results has received funding from the European Research Council (ERC) under
the Horizon Europe programme (Synergy Grant agreement N°101071505: 4D-STAR). While
partially funded by the European Union, views and opinions expressed are however
those of the authors 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. V.V. acknowledges support from the Research Foundation
Flanders (FWO) under grant agreement N°1156923N (PhD Fellowship). S.B.D. acknowledges
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement N°101034413. L.B. gratefully acknowledges
support from the European Research Council (ERC) under the Horizon Europe programme
(Calcifer; Starting Grant agreement N°101165631). J.B., M.R., S.M. and J.S.G.M have
been supported by CNES, focused on the preparation of the PLATO mission. Computations
with ESTER and TOP have made use of the HPC resources from the CALMIP supercomputing
centre (Grant 2023-P0107). This research made use of the numpy (Harris et al. 2020)
and matplotlib (Hunter 2007) Python software packages.'
article_number: A336
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J. S.G.
full_name: Mombarg, J. S.G.
last_name: Mombarg
- first_name: V.
full_name: Vanlaer, V.
last_name: Vanlaer
- first_name: Srijan B
full_name: Das, Srijan B
id: 9ce7c423-dacf-11ed-8942-e09c6cb27149
last_name: Das
orcid: 0000-0003-0896-7972
- first_name: M.
full_name: Rieutord, M.
last_name: Rieutord
- first_name: C.
full_name: Aerts, C.
last_name: Aerts
- 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: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: D. R.
full_name: Reese, D. R.
last_name: Reese
- first_name: J.
full_name: Ballot, J.
last_name: Ballot
citation:
ama: Mombarg JSG, Vanlaer V, Das SB, et al. Is a 1D perturbative method sufficient
for asteroseismic modelling of β Cephei pulsators? Implications for measurements
of rotation and internal magnetic fields. Astronomy & Astrophysics.
2025;704. doi:10.1051/0004-6361/202557247
apa: Mombarg, J. S. G., Vanlaer, V., Das, S. B., Rieutord, M., Aerts, C., Bugnet,
L. A., … Ballot, J. (2025). Is a 1D perturbative method sufficient for asteroseismic
modelling of β Cephei pulsators? Implications for measurements of rotation and
internal magnetic fields. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202557247
chicago: Mombarg, J. S.G., V. Vanlaer, Srijan B Das, M. Rieutord, C. Aerts, Lisa
Annabelle Bugnet, S. Mathis, D. R. Reese, and J. Ballot. “Is a 1D Perturbative
Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators? Implications
for Measurements of Rotation and Internal Magnetic Fields.” Astronomy &
Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202557247.
ieee: J. S. G. Mombarg et al., “Is a 1D perturbative method sufficient for
asteroseismic modelling of β Cephei pulsators? Implications for measurements of
rotation and internal magnetic fields,” Astronomy & Astrophysics, vol.
704. EDP Sciences, 2025.
ista: Mombarg JSG, Vanlaer V, Das SB, Rieutord M, Aerts C, Bugnet LA, Mathis S,
Reese DR, Ballot J. 2025. Is a 1D perturbative method sufficient for asteroseismic
modelling of β Cephei pulsators? Implications for measurements of rotation and
internal magnetic fields. Astronomy & Astrophysics. 704, A336.
mla: Mombarg, J. S. G., et al. “Is a 1D Perturbative Method Sufficient for Asteroseismic
Modelling of β Cephei Pulsators? Implications for Measurements of Rotation and
Internal Magnetic Fields.” Astronomy & Astrophysics, vol. 704, A336,
EDP Sciences, 2025, doi:10.1051/0004-6361/202557247.
short: J.S.G. Mombarg, V. Vanlaer, S.B. Das, M. Rieutord, C. Aerts, L.A. Bugnet,
S. Mathis, D.R. Reese, J. Ballot, Astronomy & Astrophysics 704 (2025).
date_created: 2026-01-04T23:01:35Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-02-16T12:14:36Z
day: '19'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202557247
ec_funded: 1
external_id:
arxiv:
- '2511.09617'
file:
- access_level: open_access
checksum: d838b4783920c43b7cc866e9cf08b383
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T08:36:28Z
date_updated: 2026-01-05T08:36:28Z
file_id: '20937'
file_name: 2025_AstronomyAstrophysics_Mombarg.pdf
file_size: 2620909
relation: main_file
success: 1
file_date_updated: 2026-01-05T08:36:28Z
has_accepted_license: '1'
intvolume: ' 704'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 914d8549-16d5-11f0-9cad-bbe6324c93a9
grant_number: '101165631'
name: 'Unveiling the mysteries of stellar dynamics: a pioneering journey in magnetoasteroseismology'
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
record:
- id: '20936'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei
pulsators? Implications for measurements of rotation and internal magnetic fields
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: 704
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20932'
abstract:
- lang: eng
text: Identifying Lyman continuum (LyC) leakers at intermediate redshifts is crucial
for understanding the properties of cosmic reionizers because the opacity of the
intergalactic medium (IGM) prevents the direct detection of LyC emission from
sources during the Epoch of Reionization (EoR). In this study, we confirm two
new LyC candidate leakers at z ∼ 3 in the Abell 2744 cluster field, with absolute
escape fractions (fesc) of 0.83−0.80+0.15 and 0.74−0.70+0.23, respectively. The
LyC emission was detected using HST/WFC3/F275W and F336W imaging. These two candidate
leakers appear to be faint (MUV = −17.61 ± 0.06 and −18.22 ± 0.10), exhibit blue
UV continuum slopes (β = −2.43 ± 0.05 and −1.92 ± 0.09), have low masses (M★ ∼ 107.51 ± 0.03
and 107.17 ± 0.15 M⊙) and Lyα equivalent widths of 90 ± 3 Å and 28 ± 12 Å, respectively.
These two LyC candidate leakers were detected in a catalog of 91 spectroscopically
confirmed sources using public spectra from the JWST and/or MUSE. We also analyzed
properties that were proposed as indirect indicators of LyC emission, such as
Lyα, the O32 ratio, and M★. We created a galaxy subsample that was selected according
to these properties, stacked the LyC observations of this subsample, and assessed
the limits of the escape fractions in the stacks. We aim to enhance our understanding
of LyC escape mechanisms and improve our predictions of the LyC fesc during the
EoR by analyzing the individual candidates and the stacks in the context of the
currently limited sample of known LyC leakers at z ∼ 3.
acknowledgement: 'We acknowledge support from the National Science Foundation of China
– 12225301, INAF Large grant “Spectroscopic survey with JWST” jand from PRIN 2022
MUR project 2022CB3PJ3 – First Light And Galaxy aSsembly (FLAGS) funded by the European
Union – Next Generation EU, and Postgraduate Scholarship Program under the grant
of China Scholarship Council. P.W. and B.V. acknowledge support from the INAF Mini
Grant ‘1.05.24.07.01 RSN1: Spatially Resolved Near-IR Emission of Intermediate-Redshift
Jellyfish Galaxies’ (PI Watson). We acknowledge A. Acebron, C. Grillo, and P. Rosati
for their fundamental contribution to the strong lensing analysis and results. We
also extend our gratitude to the JWST and HST teams for their efforts in designing,
building, and operating these transformative missions.'
article_number: A328
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Y.
full_name: Liu, Y.
last_name: Liu
- first_name: Sara
full_name: Mascia, Sara
id: edaf889c-c7cd-11ef-ab1b-bb28c431bd29
last_name: Mascia
- first_name: L.
full_name: Pentericci, L.
last_name: Pentericci
- first_name: P.
full_name: Watson, P.
last_name: Watson
- first_name: A.
full_name: Alavi, A.
last_name: Alavi
- first_name: P.
full_name: Bergamini, P.
last_name: Bergamini
- first_name: M.
full_name: Bradač, M.
last_name: Bradač
- first_name: A.
full_name: Calabrò, A.
last_name: Calabrò
- first_name: K.
full_name: Glazebrook, K.
last_name: Glazebrook
- first_name: A.
full_name: Henry, A.
last_name: Henry
- first_name: M.
full_name: Llerena, M.
last_name: Llerena
- first_name: E.
full_name: Merlin, E.
last_name: Merlin
- first_name: B.
full_name: Metha, B.
last_name: Metha
- first_name: T.
full_name: Nanayakkara, T.
last_name: Nanayakkara
- first_name: L.
full_name: Napolitano, L.
last_name: Napolitano
- first_name: N.
full_name: Roy, N.
last_name: Roy
- first_name: B.
full_name: Siana, B.
last_name: Siana
- first_name: E.
full_name: Vanzella, E.
last_name: Vanzella
- first_name: B.
full_name: Vulcani, B.
last_name: Vulcani
- first_name: X.
full_name: Wang, X.
last_name: Wang
citation:
ama: Liu Y, Mascia S, Pentericci L, et al. A Lyman continuum analysis of ∼100 galaxies
at z spec∼ 3 in the Abell 2744 cluster field. Astronomy & Astrophysics.
2025;704. doi:10.1051/0004-6361/202556410
apa: Liu, Y., Mascia, S., Pentericci, L., Watson, P., Alavi, A., Bergamini, P.,
… Wang, X. (2025). A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in
the Abell 2744 cluster field. Astronomy & Astrophysics. EDP Sciences.
https://doi.org/10.1051/0004-6361/202556410
chicago: Liu, Y., Sara Mascia, L. Pentericci, P. Watson, A. Alavi, P. Bergamini,
M. Bradač, et al. “A Lyman Continuum Analysis of ∼100 Galaxies at z Spec∼ 3 in
the Abell 2744 Cluster Field.” Astronomy & Astrophysics. EDP Sciences,
2025. https://doi.org/10.1051/0004-6361/202556410.
ieee: Y. Liu et al., “A Lyman continuum analysis of ∼100 galaxies at z spec∼
3 in the Abell 2744 cluster field,” Astronomy & Astrophysics, vol.
704. EDP Sciences, 2025.
ista: Liu Y, Mascia S, Pentericci L, Watson P, Alavi A, Bergamini P, Bradač M, Calabrò
A, Glazebrook K, Henry A, Llerena M, Merlin E, Metha B, Nanayakkara T, Napolitano
L, Roy N, Siana B, Vanzella E, Vulcani B, Wang X. 2025. A Lyman continuum analysis
of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field. Astronomy &
Astrophysics. 704, A328.
mla: Liu, Y., et al. “A Lyman Continuum Analysis of ∼100 Galaxies at z Spec∼ 3 in
the Abell 2744 Cluster Field.” Astronomy & Astrophysics, vol. 704,
A328, EDP Sciences, 2025, doi:10.1051/0004-6361/202556410.
short: Y. Liu, S. Mascia, L. Pentericci, P. Watson, A. Alavi, P. Bergamini, M. Bradač,
A. Calabrò, K. Glazebrook, A. Henry, M. Llerena, E. Merlin, B. Metha, T. Nanayakkara,
L. Napolitano, N. Roy, B. Siana, E. Vanzella, B. Vulcani, X. Wang, Astronomy &
Astrophysics 704 (2025).
date_created: 2026-01-04T23:01:35Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-02-16T12:14:52Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.1051/0004-6361/202556410
external_id:
arxiv:
- '2507.11045'
file:
- access_level: open_access
checksum: 3e6061f3c4bfb521b3333ea4913c241a
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T09:26:17Z
date_updated: 2026-01-05T09:26:17Z
file_id: '20938'
file_name: 2025_AstronomyAstrophysics_Liu.pdf
file_size: 4642530
relation: main_file
success: 1
file_date_updated: 2026-01-05T09:26:17Z
has_accepted_license: '1'
intvolume: ' 704'
language:
- iso: eng
month: '12'
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'
scopus_import: '1'
status: public
title: A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744
cluster field
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: 704
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20933'
abstract:
- lang: eng
text: Photo-responsive systems based on azobenzenes usually require UV light for
E→Z isomerization, limiting their applicability, especially in biomedical contexts.
Disequilibration by sensitization of azobenzene under confinement (DESC) has recently
emerged as a supramolecular strategy to bypass this limitation without the need
to derivatize the azobenzene scaffold. Here, we expand DESC to water-soluble azopolymers
obtained by RAFT polymerization and systematically investigate the interplay between
the polymer structure and DESC efficiency. Using this approach, we achieved as
much as 85% of the direct photoexcitation (UV) switching efficiency, while utilizing
low-energy (yellow) light. These results establish general design principles for
combining DESC with polymeric systems, opening new opportunities for the development
of functional materials driven with low-energy light.
acknowledgement: "This work is supported by the European Research Council (Consolidator
Grand project MULTIMODAL, no. 101045223), the Research Council of Finland Center
of Excellence “Life-Inspired Hybrid Materials Research” (LIBER, no. 346107) and
the Research Council of Finland Flagship Programme on Photonics Research and Innovation
(PREIN, no. 320165). H.M. gratefully acknowledges Oommen Podivan for providing access
to their Zetasizer for DLS measurements and the Faculty of Medicine and Health Technologies
at Tampere University for access to their laboratory facilities. R.K. acknowledges
funding through the Award for Research Cooperation and High Excellence in Science
(ARCHES) from the Federal German Ministry for Education and Research. S.H. acknowledges
financial support through the profi7 profiling action SUSBIO from the Research Council
of Finland (no. 352754).\r\nOpen access publishing facilitated by Tampereen yliopisto
ja Tampereen ammattikorkeakoulu, as part of the Wiley - FinELib agreement."
article_number: e23447
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Henning Jörn
full_name: Meteling, Henning Jörn
last_name: Meteling
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Satu
full_name: Häkkinen, Satu
last_name: Häkkinen
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Arri
full_name: Priimagi, Arri
last_name: Priimagi
citation:
ama: Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. Sensitized disequilibration
of water-soluble azopolymers. Angewandte Chemie International Edition.
2025. doi:10.1002/anie.202523447
apa: Meteling, H. J., Gemen, J., Häkkinen, S., Klajn, R., & Priimagi, A. (2025).
Sensitized disequilibration of water-soluble azopolymers. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.202523447
chicago: Meteling, Henning Jörn, Julius Gemen, Satu Häkkinen, Rafal Klajn, and Arri
Priimagi. “Sensitized Disequilibration of Water-Soluble Azopolymers.” Angewandte
Chemie International Edition. Wiley, 2025. https://doi.org/10.1002/anie.202523447.
ieee: H. J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, and A. Priimagi, “Sensitized
disequilibration of water-soluble azopolymers,” Angewandte Chemie International
Edition. Wiley, 2025.
ista: Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. 2025. Sensitized disequilibration
of water-soluble azopolymers. Angewandte Chemie International Edition., e23447.
mla: Meteling, Henning Jörn, et al. “Sensitized Disequilibration of Water-Soluble
Azopolymers.” Angewandte Chemie International Edition, e23447, Wiley, 2025,
doi:10.1002/anie.202523447.
short: H.J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, A. Priimagi, Angewandte Chemie
International Edition (2025).
date_created: 2026-01-04T23:01:35Z
date_published: 2025-12-23T00:00:00Z
date_updated: 2026-01-05T09:42:56Z
day: '23'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1002/anie.202523447
external_id:
pmid:
- '41437660'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.202523447
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7bf494dc-9f16-11ee-852c-9fe37e3f50f0
grant_number: '713490'
name: 'Integrating Molecular Photoswitches with PH-Feedback Mechanisms: Towards
Life-like Materials'
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensitized disequilibration of water-soluble azopolymers
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
year: '2025'
...
---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20934'
abstract:
- lang: eng
text: ' Supervised learning for causal discovery from observational data often achieves
competitive performance despite seemingly avoiding the explicit assumptions that
traditional methods require for identifiability. In this work, we analyze CSIvA
(Ke et al., 2023) on bivariate causal models, a transformer architecture for amortized
inference promising to train on synthetic data and transfer to real ones. First,
we bridge the gap with identifiability theory, showing that the training distribution
implicitly defines a prior on the causal model of the test observations: consistent
with classical approaches, good performance is achieved when we have a good prior
on the test data, and the underlying model is identifiable. Second, we find that
CSIvA can not generalize to classes of causal models unseen during training: to
overcome this limitation, we theoretically and empirically analyze \textit{when}
training CSIvA on datasets generated by multiple identifiable causal models with
different structural assumptions improves its generalization at test time. Overall,
we find that amortized causal discovery still adheres to identifiability theory,
violating the previous hypothesis from Lopez-Paz et al. (2015) that supervised
learning methods could overcome its restrictions.'
alternative_title:
- TMLR
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Francesco
full_name: Montagna, Francesco
id: 353afc8e-19f4-11f0-9db9-811f1723c83f
last_name: Montagna
- first_name: Maximilian T
full_name: Cairney-Leeming, Maximilian T
id: 2214a80c-31f8-11ee-a48d-cf52cc58759b
last_name: Cairney-Leeming
- first_name: Dhanya
full_name: Sridhar, Dhanya
last_name: Sridhar
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Montagna F, Cairney-Leeming MT, Sridhar D, Locatello F. Demystifying amortized
causal discovery with transformers. Transactions on Machine Learning Research.
2025.
apa: Montagna, F., Cairney-Leeming, M. T., Sridhar, D., & Locatello, F. (2025).
Demystifying amortized causal discovery with transformers. Transactions on
Machine Learning Research. ML Research Press.
chicago: Montagna, Francesco, Maximilian T Cairney-Leeming, Dhanya Sridhar, and
Francesco Locatello. “Demystifying Amortized Causal Discovery with Transformers.”
Transactions on Machine Learning Research. ML Research Press, 2025.
ieee: F. Montagna, M. T. Cairney-Leeming, D. Sridhar, and F. Locatello, “Demystifying
amortized causal discovery with transformers,” Transactions on Machine Learning
Research. ML Research Press, 2025.
ista: Montagna F, Cairney-Leeming MT, Sridhar D, Locatello F. 2025. Demystifying
amortized causal discovery with transformers. Transactions on Machine Learning
Research.
mla: Montagna, Francesco, et al. “Demystifying Amortized Causal Discovery with Transformers.”
Transactions on Machine Learning Research, ML Research Press, 2025.
short: F. Montagna, M.T. Cairney-Leeming, D. Sridhar, F. Locatello, Transactions
on Machine Learning Research (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:35Z
date_published: 2025-12-18T00:00:00Z
date_updated: 2026-01-05T09:54:59Z
day: '18'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2405.16924'
file:
- access_level: open_access
checksum: 968c471bb1f682cf823b2d4cadea8a3f
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T09:51:28Z
date_updated: 2026-01-05T09:51:28Z
file_id: '20939'
file_name: 2025_PMLR_Montagna.pdf
file_size: 1030280
relation: main_file
success: 1
file_date_updated: 2026-01-05T09:51:28Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Transactions on Machine Learning Research
publication_identifier:
eissn:
- 2835-8856
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/francescomontagna/learning-to-induce.git
scopus_import: '1'
status: public
title: Demystifying amortized causal discovery with transformers
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
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20935'
abstract:
- lang: eng
text: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice
to investigate the structures of biomolecules in their native context. However,
challenges remain for the efficient production and sharing of large-scale cryo-ET
datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB)
milling with recent advances in cryo-ET acquisition and processing to generate
a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii,
which we provide as a community resource to drive method development and inspire
biological discovery. To assay data quality, we performed subtomogram averaging
of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200
kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem
II, and mitochondrial ATP synthase. The majority of these density maps reached
sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset
as well as the promise of modern cryo-ET workflows and open data sharing to empower
visual proteomics.
acknowledgement: Calculations were performed at the Max Planck Institute of Biochemistry
and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF)
in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing
center at the University of Basel, Switzerland; and at Thermo Fisher Scientific,
in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific.
All lamella preparations and tilt-series collections used in this work were conducted
at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios
microscopes. This work was also supported by the ERC consolidator grant “cryOcean”
(fulfilled by the Swiss State Secretariat for Education, Research and Innovation,
M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E.
and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T.,
an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim
Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ron
full_name: Kelley, Ron
last_name: Kelley
- first_name: Sagar
full_name: Khavnekar, Sagar
last_name: Khavnekar
- first_name: Ricardo D.
full_name: Righetto, Ricardo D.
last_name: Righetto
- first_name: Jessica
full_name: Heebner, Jessica
last_name: Heebner
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Xianjun
full_name: Zhang, Xianjun
last_name: Zhang
- first_name: Saikat
full_name: Chakraborty, Saikat
last_name: Chakraborty
- first_name: Grigory
full_name: Tagiltsev, Grigory
last_name: Tagiltsev
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Sofie
full_name: Van Dorst, Sofie
last_name: Van Dorst
- first_name: Florent
full_name: Waltz, Florent
last_name: Waltz
- first_name: Caitlyn L.
full_name: Mccafferty, Caitlyn L.
last_name: Mccafferty
- first_name: Lorenz
full_name: Lamm, Lorenz
last_name: Lamm
- first_name: Simon
full_name: Zufferey, Simon
last_name: Zufferey
- first_name: Philippe
full_name: Van Der Stappen, Philippe
last_name: Van Der Stappen
- first_name: Hugo
full_name: Van Den Hoek, Hugo
last_name: Van Den Hoek
- first_name: Wojciech
full_name: Wietrzynski, Wojciech
last_name: Wietrzynski
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John A.G.
full_name: Briggs, John A.G.
last_name: Briggs
- first_name: Jürgen M.
full_name: Plitzko, Jürgen M.
last_name: Plitzko
- first_name: Benjamin D.
full_name: Engel, Benjamin D.
last_name: Engel
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
citation:
ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics
with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular
Cell. doi:10.1016/j.molcel.2025.11.029
apa: Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X.,
… Kotecha, A. (n.d.). Toward community-driven visual proteomics with large-scale
cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.
Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029
chicago: Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin
Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual
Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.”
Molecular Cell. Elsevier, n.d. https://doi.org/10.1016/j.molcel.2025.11.029.
ieee: R. Kelley et al., “Toward community-driven visual proteomics with large-scale
cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell.
Elsevier.
ista: Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty
S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey
S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG,
Plitzko JM, Engel BD, Kotecha A. Toward community-driven visual proteomics with
large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.
mla: Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale
Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell,
Elsevier, doi:10.1016/j.molcel.2025.11.029.
short: R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S.
Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty,
L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P.
Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular
Cell (n.d.).
date_created: 2026-01-04T23:01:36Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-01-05T08:32:47Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.11.029
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2025.11.029
month: '12'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward community-driven visual proteomics with large-scale cryo-electron tomography
of Chlamydomonas reinhardtii
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
year: '2025'
...
---
OA_place: repository
OA_type: gold
_id: '20936'
abstract:
- lang: eng
text: "Supplementary material for Mombarg et al. (2025, A&A). Title: \"Is a 1D perturbative
method sufficient for asteroseismic modelling of \r\n~Cephei pulsators? Implications
for measurements of rotation and internal magnetic fields\"\r\n\r\nContent:\r\n-
Non-rotating ESTER models and associated .GSM models. (Xini = 0.71, Zini = 0.014,
vertical/horizonal viscosity 10^7 cm^2/s, vertical chemical diffusion 10^4 cm^2/s
for evolution model. More details on the ESTER models can be found in the ESTER
manual.\r\n\r\n- Rotational asymmetries computed with StORM and TOP in 1/d, and
the central m=0 frequency from TOP in 1/d. (all_A*_new.pkl)\r\n\r\n- Magnetic
asymmetries in 1/d for different obliquity angles between 0 and 90 deg for ZAMS
and MAMS model, for B_0 = 75 kG. *_nu key gives unperturbed mode frequencies,
*_npg the radial order (asym_dict.pkl, asym_dict_evol.pkl)"
article_processing_charge: No
author:
- first_name: Joey
full_name: Mombarg, Joey
last_name: Mombarg
- first_name: Vincent
full_name: Vanlaer, Vincent
last_name: Vanlaer
- first_name: Srijan B
full_name: Das, Srijan B
id: 9ce7c423-dacf-11ed-8942-e09c6cb27149
last_name: Das
orcid: 0000-0003-0896-7972
- first_name: Michel
full_name: Rieutord, Michel
last_name: Rieutord
- first_name: Conny
full_name: Aerts, Conny
last_name: Aerts
- 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: Stephane
full_name: Mathis, Stephane
last_name: Mathis
- first_name: Daniel
full_name: Reese, Daniel
last_name: Reese
- first_name: Jerome
full_name: Ballot, Jerome
last_name: Ballot
citation:
ama: Mombarg J, Vanlaer V, Das SB, et al. Is a 1D perturbative method sufficient
for asteroseismic modelling of β Cephei pulsators? 2025. doi:10.5281/ZENODO.17580178
apa: Mombarg, J., Vanlaer, V., Das, S. B., Rieutord, M., Aerts, C., Bugnet, L. A.,
… Ballot, J. (2025). Is a 1D perturbative method sufficient for asteroseismic
modelling of β Cephei pulsators? Zenodo. https://doi.org/10.5281/ZENODO.17580178
chicago: Mombarg, Joey, Vincent Vanlaer, Srijan B Das, Michel Rieutord, Conny Aerts,
Lisa Annabelle Bugnet, Stephane Mathis, Daniel Reese, and Jerome Ballot. “Is a
1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators?”
Zenodo, 2025. https://doi.org/10.5281/ZENODO.17580178.
ieee: J. Mombarg et al., “Is a 1D perturbative method sufficient for asteroseismic
modelling of β Cephei pulsators?” Zenodo, 2025.
ista: Mombarg J, Vanlaer V, Das SB, Rieutord M, Aerts C, Bugnet LA, Mathis S, Reese
D, Ballot J. 2025. Is a 1D perturbative method sufficient for asteroseismic modelling
of β Cephei pulsators?, Zenodo, 10.5281/ZENODO.17580178.
mla: Mombarg, Joey, et al. Is a 1D Perturbative Method Sufficient for Asteroseismic
Modelling of β Cephei Pulsators? Zenodo, 2025, doi:10.5281/ZENODO.17580178.
short: J. Mombarg, V. Vanlaer, S.B. Das, M. Rieutord, C. Aerts, L.A. Bugnet, S.
Mathis, D. Reese, J. Ballot, (2025).
date_created: 2026-01-05T08:39:33Z
date_published: 2025-11-11T00:00:00Z
date_updated: 2026-02-16T12:14:36Z
day: '11'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.5281/ZENODO.17580178
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.17580178
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Zenodo
related_material:
record:
- id: '20931'
relation: used_in_publication
status: public
status: public
title: Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20940'
abstract:
- lang: eng
text: These are the raw data files that supplement our study of mode dispersion
with magnetic field of a cavity-magnonics system containing chromium trichloride
on coplanar waveguide resonator.
article_processing_charge: No
author:
- first_name: Supriya
full_name: Mandal, Supriya
last_name: Mandal
- first_name: Krishnendu
full_name: Maji, Krishnendu
id: 76bc9e9f-ba0b-11ee-8184-90edabd17a58
last_name: Maji
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Souvik
full_name: Sasmal, Souvik
last_name: Sasmal
- first_name: Soham
full_name: Manni, Soham
last_name: Manni
- first_name: John
full_name: Jesudasan, John
last_name: Jesudasan
- first_name: Pratap
full_name: Raychaudhuri, Pratap
last_name: Raychaudhuri
- first_name: Arumugam
full_name: Thamizhavel, Arumugam
last_name: Thamizhavel
- first_name: Mandar M.
full_name: Deshmukh, Mandar M.
last_name: Deshmukh
citation:
ama: Mandal S, Maji K, Kapoor L, et al. Mode dispersion with magnetic field in a
cavity-magnonics system. 2025. doi:10.5281/ZENODO.15321721
apa: Mandal, S., Maji, K., Kapoor, L., Sasmal, S., Manni, S., Jesudasan, J., … Deshmukh,
M. M. (2025). Mode dispersion with magnetic field in a cavity-magnonics system.
Zenodo. https://doi.org/10.5281/ZENODO.15321721
chicago: Mandal, Supriya, Krishnendu Maji, Lucky Kapoor, Souvik Sasmal, Soham Manni,
John Jesudasan, Pratap Raychaudhuri, Arumugam Thamizhavel, and Mandar M. Deshmukh.
“Mode Dispersion with Magnetic Field in a Cavity-Magnonics System.” Zenodo, 2025.
https://doi.org/10.5281/ZENODO.15321721.
ieee: S. Mandal et al., “Mode dispersion with magnetic field in a cavity-magnonics
system.” Zenodo, 2025.
ista: Mandal S, Maji K, Kapoor L, Sasmal S, Manni S, Jesudasan J, Raychaudhuri P,
Thamizhavel A, Deshmukh MM. 2025. Mode dispersion with magnetic field in a cavity-magnonics
system, Zenodo, 10.5281/ZENODO.15321721.
mla: Mandal, Supriya, et al. Mode Dispersion with Magnetic Field in a Cavity-Magnonics
System. Zenodo, 2025, doi:10.5281/ZENODO.15321721.
short: S. Mandal, K. Maji, L. Kapoor, S. Sasmal, S. Manni, J. Jesudasan, P. Raychaudhuri,
A. Thamizhavel, M.M. Deshmukh, (2025).
date_created: 2026-01-05T10:00:06Z
date_published: 2025-05-02T00:00:00Z
date_updated: 2026-01-05T10:07:04Z
day: '02'
department:
- _id: MaIb
- _id: JoFi
doi: 10.5281/ZENODO.15321721
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.15321721
month: '05'
oa: 1
oa_version: Submitted Version
publisher: Zenodo
related_material:
record:
- id: '20927'
relation: used_in_publication
status: public
status: public
title: Mode dispersion with magnetic field in a cavity-magnonics system
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20960'
abstract:
- lang: eng
text: A linker unit was designed and synthesized that can serve both as a hairpin
turn in a DNA duplex and anchor point for an aromatic helical foldamer mimicking
the shape and surface properties of B‐DNA. Methods were developed to synthesize
natural/non‐natural chimeric molecules combining foldamer and DNA segments. The
ability of the linker to position the foldamer helix and the duplex DNA so that
their rims and grooves are in register, despite their completely different chemical
nature, was demonstrated using single crystal X‐ray diffraction, circular dichroism
and molecular models. Bio‐layer interferometry confirmed that artificial hairpin
DNA duplexes keep their ability to bind to DNA binding proteins. The chimeric
molecules may pave the way to competitive inhibitors of protein‐DNA interactions
involving sequence‐selective DNA‐binding proteins.
article_number: e202505273
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Manuel
full_name: Loos, Manuel
last_name: Loos
- first_name: Felix
full_name: Xu, Felix
last_name: Xu
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Tulika
full_name: Chakrabortty, Tulika
last_name: Chakrabortty
- first_name: Céline
full_name: Douat, Céline
last_name: Douat
- first_name: David B.
full_name: Konrad, David B.
last_name: Konrad
- first_name: Melis
full_name: Cabbar, Melis
last_name: Cabbar
- first_name: Johannes
full_name: Singer, Johannes
last_name: Singer
- first_name: Valentina
full_name: Corvaglia, Valentina
last_name: Corvaglia
- first_name: Thomas
full_name: Carell, Thomas
last_name: Carell
- first_name: Ivan
full_name: Huc, Ivan
last_name: Huc
citation:
ama: Loos M, Xu F, Mandal PK, et al. Interfacing B‐DNA and DNA mimic foldamers.
Angewandte Chemie International Edition. 2025;64(31). doi:10.1002/anie.202505273
apa: Loos, M., Xu, F., Mandal, P. K., Chakrabortty, T., Douat, C., Konrad, D. B.,
… Huc, I. (2025). Interfacing B‐DNA and DNA mimic foldamers. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.202505273
chicago: Loos, Manuel, Felix Xu, Pradeep K Mandal, Tulika Chakrabortty, Céline Douat,
David B. Konrad, Melis Cabbar, et al. “Interfacing B‐DNA and DNA Mimic Foldamers.”
Angewandte Chemie International Edition. Wiley, 2025. https://doi.org/10.1002/anie.202505273.
ieee: M. Loos et al., “Interfacing B‐DNA and DNA mimic foldamers,” Angewandte
Chemie International Edition, vol. 64, no. 31. Wiley, 2025.
ista: Loos M, Xu F, Mandal PK, Chakrabortty T, Douat C, Konrad DB, Cabbar M, Singer
J, Corvaglia V, Carell T, Huc I. 2025. Interfacing B‐DNA and DNA mimic foldamers.
Angewandte Chemie International Edition. 64(31), e202505273.
mla: Loos, Manuel, et al. “Interfacing B‐DNA and DNA Mimic Foldamers.” Angewandte
Chemie International Edition, vol. 64, no. 31, e202505273, Wiley, 2025, doi:10.1002/anie.202505273.
short: M. Loos, F. Xu, P.K. Mandal, T. Chakrabortty, C. Douat, D.B. Konrad, M. Cabbar,
J. Singer, V. Corvaglia, T. Carell, I. Huc, Angewandte Chemie International Edition
64 (2025).
date_created: 2026-01-08T07:04:48Z
date_published: 2025-07-28T00:00:00Z
date_updated: 2026-01-19T11:07:53Z
day: '28'
ddc:
- '540'
doi: 10.1002/anie.202505273
extern: '1'
external_id:
pmid:
- '40346004'
has_accepted_license: '1'
intvolume: ' 64'
issue: '31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.202505273
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interfacing B‐DNA and DNA mimic foldamers
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: 64
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20976'
abstract:
- lang: eng
text: We present an experimental demonstration of an impedance-engineered Josephson
parametric amplifier (IEJPA) fabricated in a single-step lithography process.
Impedance-engineering is implemented using a lumped-element series LC circuit.
We use a simpler lithography process where the entire device—impedance transformer
and Josephson parametric amplifier (JPA)—is patterned in a single electron beam
lithography step, followed by a double-angle Dolan-bridge technique for Al–AlOx–Al
deposition. We observe amplification with 18 dB gain over a wide 400 MHz bandwidth
centered around 5.3 GHz with added noise approaching the quantum limit, and a
saturation power of −114 dBm. To accurately explain our experimental results,
we extend existing theories for IEJPAs to incorporate the full sine nonlinearity
of both the JPA and the transformer. Our work provides a route to simpler realization
of broadband JPAs and a theoretical foundation for a regime of JPA operation that
has been less explored in literature.
acknowledgement: The authors acknowledge receiving support from the Space Technology
Cell at IISc and ISRO through the project STC-0444(2022) and the Ministry of Electronics
and Information Technology of the Government of India, under the centre of Excellence
of Quantum Technology at the Indian Institute of Science, as well as the office
of Principle Scientific Advisor, Government of India. S.H. and A.P. acknowledge
the support of the Kishore Vaigyanik Protsahan Yojana (KVPY). A.S. acknowledges
the support of a New Faculty Initiation Grant (NFIG) from IIT Madras.
article_number: '254001'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lipi
full_name: Patel, Lipi
last_name: Patel
- first_name: Samarth
full_name: Hawaldar, Samarth
id: 221708e1-1ff6-11ee-9fa6-85146607433e
last_name: Hawaldar
orcid: 0000-0002-1965-4309
- first_name: Aditya
full_name: Panikkar, Aditya
last_name: Panikkar
- first_name: Athreya
full_name: Shankar, Athreya
last_name: Shankar
- first_name: Baladitya
full_name: Suri, Baladitya
last_name: Suri
citation:
ama: Patel L, Hawaldar S, Panikkar A, Shankar A, Suri B. Impedance-engineered Josephson
parametric amplifier with single-step lithography. Applied Physics Letters.
2025;127(25). doi:10.1063/5.0290636
apa: Patel, L., Hawaldar, S., Panikkar, A., Shankar, A., & Suri, B. (2025).
Impedance-engineered Josephson parametric amplifier with single-step lithography.
Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0290636
chicago: Patel, Lipi, Samarth Hawaldar, Aditya Panikkar, Athreya Shankar, and Baladitya
Suri. “Impedance-Engineered Josephson Parametric Amplifier with Single-Step Lithography.”
Applied Physics Letters. AIP Publishing, 2025. https://doi.org/10.1063/5.0290636.
ieee: L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, and B. Suri, “Impedance-engineered
Josephson parametric amplifier with single-step lithography,” Applied Physics
Letters, vol. 127, no. 25. AIP Publishing, 2025.
ista: Patel L, Hawaldar S, Panikkar A, Shankar A, Suri B. 2025. Impedance-engineered
Josephson parametric amplifier with single-step lithography. Applied Physics Letters.
127(25), 254001.
mla: Patel, Lipi, et al. “Impedance-Engineered Josephson Parametric Amplifier with
Single-Step Lithography.” Applied Physics Letters, vol. 127, no. 25, 254001,
AIP Publishing, 2025, doi:10.1063/5.0290636.
short: L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, B. Suri, Applied Physics
Letters 127 (2025).
date_created: 2026-01-11T23:01:34Z
date_published: 2025-12-22T00:00:00Z
date_updated: 2026-01-12T09:57:53Z
day: '22'
department:
- _id: JoFi
doi: 10.1063/5.0290636
external_id:
arxiv:
- '2507.09298'
intvolume: ' 127'
issue: '25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.09298
month: '12'
oa: 1
oa_version: Preprint
publication: Applied Physics Letters
publication_identifier:
eissn:
- 1077-3118
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impedance-engineered Josephson parametric amplifier with single-step lithography
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20977'
abstract:
- lang: eng
text: Hippocampal sharp-wave ripples (SPW-Rs) are high-frequency oscillations critical
for memory consolidation. Despite extensive characterization in rodents, their
detection in humans is limited by coarse spatial sampling, interictal epileptiform
discharges (IEDs), and a lack of consensus on human ripple localization and morphology.
Here, we demonstrate that mouse and human hippocampal ripples share spatial, spectral
and temporal features, which are clearly distinct from IEDs. In recordings from
male APP/PS1 mice, SPW-Rs were distinguishable from IEDs by multiple criteria.
Hippocampal ripples recorded during NREM sleep in female and male surgical epilepsy
patients exhibited similar narrowband frequency peaks and multiple ripple cycles
in the CA1 and subiculum regions. Conversely, IEDs showed a broad spatial extent
and wide-band frequency power. We developed a semi-automated, ripple curation
toolbox (ripmap) to separate event waveforms by low-dimensional embedding to reduce
false-positive rate in selected ripple channels. Our approach improves ripple
detection and provides a firm foundation for future human memory research.
acknowledgement: We thank Karl Rössler and Sebastian Brandner for the human SEEG implantations;
Katja Kobow for providing the histopathological findings of the patients; Jay Jeschke
for help with human electrode localization; Esha Brahmbhatt and Deren Aykan for
help with animal habituation; Mursel Karadas for the rodent treadmill design; Nicholas
Paleologos, Noam Nitzan, Michael D Hadler and Samuel McKenzie for rating events
in a human ripple survey included in a previous version of the manuscript; Nicholas
Paleologos for sharing NYU iEEG data for validating UMAP parameters; Julio Esparza
for help on the topological analysis through discussions; Thomas Hainmüller, Yiyao
Zhang and Mursel Karadas for feedback on the manuscript. We would like to acknowledge
Corticale SRL (Genoa, Italy) for providing the SiNAPS probes, and NeuroNexus (Ann
Arbor, MI) for their contribution of the data acquisition system and Radiens software.
We further acknowledge both Corticale and NeuroNexus for training and support making
this research possible. This work was supported by the German Research Foundation
(DFG; Walter Benjamin Fellowship MA 10301/1-1, A.M.), NYU Langone Health Finding
a Cure for Epilepsy and Seizures (FACES, A.M.), the NOMIS Fellowship (A.N.-O.),
the National Institutes of Health (R01NS127954, K23NS104252, A.L.; MH122391, U19NS107616,
R01MH139216 G.B.,), and the NYU Department of Neurology (A.L.).
article_number: '11636'
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna
full_name: Maslarova, Anna
last_name: Maslarova
- first_name: Jiyun N.
full_name: Shin, Jiyun N.
last_name: Shin
- first_name: Andrea C
full_name: Navas Olivé, Andrea C
id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce
last_name: Navas Olivé
orcid: 0000-0002-9280-8597
- first_name: Mihály
full_name: Vöröslakos, Mihály
last_name: Vöröslakos
- first_name: Hajo
full_name: Hamer, Hajo
last_name: Hamer
- first_name: Arnd
full_name: Doerfler, Arnd
last_name: Doerfler
- first_name: Simon
full_name: Henin, Simon
last_name: Henin
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
- first_name: Anli
full_name: Liu, Anli
last_name: Liu
citation:
ama: Maslarova A, Shin JN, Navas Olivé AC, et al. Spatiotemporal patterns differentiate
hippocampal sharp-wave ripples from interictal epileptiform discharges in mice
and humans. Nature Communications. 2025;16. doi:10.1038/s41467-025-66562-6
apa: Maslarova, A., Shin, J. N., Navas Olivé, A. C., Vöröslakos, M., Hamer, H.,
Doerfler, A., … Liu, A. (2025). Spatiotemporal patterns differentiate hippocampal
sharp-wave ripples from interictal epileptiform discharges in mice and humans.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-66562-6
chicago: Maslarova, Anna, Jiyun N. Shin, Andrea C Navas Olivé, Mihály Vöröslakos,
Hajo Hamer, Arnd Doerfler, Simon Henin, György Buzsáki, and Anli Liu. “Spatiotemporal
Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform
Discharges in Mice and Humans.” Nature Communications. Springer Nature,
2025. https://doi.org/10.1038/s41467-025-66562-6.
ieee: A. Maslarova et al., “Spatiotemporal patterns differentiate hippocampal
sharp-wave ripples from interictal epileptiform discharges in mice and humans,”
Nature Communications, vol. 16. Springer Nature, 2025.
ista: Maslarova A, Shin JN, Navas Olivé AC, Vöröslakos M, Hamer H, Doerfler A, Henin
S, Buzsáki G, Liu A. 2025. Spatiotemporal patterns differentiate hippocampal sharp-wave
ripples from interictal epileptiform discharges in mice and humans. Nature Communications.
16, 11636.
mla: Maslarova, Anna, et al. “Spatiotemporal Patterns Differentiate Hippocampal
Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.”
Nature Communications, vol. 16, 11636, Springer Nature, 2025, doi:10.1038/s41467-025-66562-6.
short: A. Maslarova, J.N. Shin, A.C. Navas Olivé, M. Vöröslakos, H. Hamer, A. Doerfler,
S. Henin, G. Buzsáki, A. Liu, Nature Communications 16 (2025).
date_created: 2026-01-11T23:01:35Z
date_published: 2025-12-30T00:00:00Z
date_updated: 2026-01-12T09:31:56Z
day: '30'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-025-66562-6
external_id:
pmid:
- '39975118'
file:
- access_level: open_access
checksum: a8a1670e197484382e087be60f643945
content_type: application/pdf
creator: dernst
date_created: 2026-01-12T09:30:15Z
date_updated: 2026-01-12T09:30:15Z
file_id: '20978'
file_name: 2025_NatureComm_Maslarova.pdf
file_size: 7629997
relation: main_file
success: 1
file_date_updated: 2026-01-12T09:30:15Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal
epileptiform discharges in mice and humans
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...