---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21480'
abstract:
- lang: eng
text: We present and test a protocol to learn the matrix-product operator (MPO)
representation of an experimentally prepared quantum state. The protocol takes
as input classical shadows corresponding to local randomized measurements, and
outputs the tensors of an MPO maximizing a suitably defined fidelity with the
experimental state. The tensor optimization is carried out sequentially, similarly
to the well-known density matrix renormalization group algorithm. Our approach
is provably efficient under certain technical conditions expected to be met in
short-range correlated states and in typical noisy experimental settings. Under
the same conditions, we also provide an efficient scheme to estimate fidelities
between the learned and the experimental states. We experimentally demonstrate
our protocol by learning entangled quantum states of up to N = 96 qubits in a
superconducting quantum processor. Our method upgrades classical shadows to large-scale
quantum computation and simulation experiments.
acknowledgement: "We acknowledge insightful discussions with Antoine Browaeys, Mari
Carmen Bañuls, Soonwon Choi, Thierry Lahaye, Daniel Stilck-França, Georgios Styliaris,
and Xavier Waintal. The experimental data have been collected using the Qiskit library
[103], and have been postprocessed using the RandomMeas [104] and ITensor [105]
libraries. The work of M. V. and B. V. was funded by the French National Research
Agency via the JCJC project QRand (No. ANR-20-CE47-0005), and via the research programs
Plan France 2030 EPIQ (No. ANR-22-\r\nPETQ-0007), QUBITAF (No. ANR-22-PETQ-0004),
and HQI (No. ANR-22-PNCQ-0002). We acknowledge the use of IBM Quantum Credits for
this work. M. L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.
The work of C. L. was funded by the French National Research Agency via the PRC
project ESQuisses (No. ANR-20-CE47-0014-01). J. I. C.\r\nacknowledges funding from
the Federal Ministry of Education and Research Germany (BMBF) via the project FermiQP
(No. 13N15889). Work at MPQ is part of the Munich Quantum Valley, which is supported
by the Bavarian state government with funds from the Hightech Agenda\r\nBayern Plus.
P. Z. acknowledges support by the European Union’s Horizon Europe research and innovation
program under Grant Agreement No. 101113690 (PASQANS2). The work of L. P. was funded
by the European Union (ERC, QUANTHEM, No. 101114881). We acknowledge support\r\nby
the Erwin Schrödinger International Institute for Mathematics and Physics (ESI)."
article_number: '090801'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Matteo
full_name: Votto, Matteo
last_name: Votto
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Cécilia
full_name: Lancien, Cécilia
last_name: Lancien
- first_name: J. Ignacio
full_name: Cirac, J. Ignacio
last_name: Cirac
- first_name: Peter
full_name: Zoller, Peter
last_name: Zoller
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Lorenzo
full_name: Piroli, Lorenzo
last_name: Piroli
- first_name: Benoît
full_name: Vermersch, Benoît
last_name: Vermersch
citation:
ama: Votto M, Ljubotina M, Lancien C, et al. Learning mixed quantum states in large-scale
experiments. Physical Review Letters. 2026;136(9). doi:10.1103/rbg2-f61m
apa: Votto, M., Ljubotina, M., Lancien, C., Cirac, J. I., Zoller, P., Serbyn, M.,
… Vermersch, B. (2026). Learning mixed quantum states in large-scale experiments.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/rbg2-f61m
chicago: Votto, Matteo, Marko Ljubotina, Cécilia Lancien, J. Ignacio Cirac, Peter
Zoller, Maksym Serbyn, Lorenzo Piroli, and Benoît Vermersch. “Learning Mixed Quantum
States in Large-Scale Experiments.” Physical Review Letters. American Physical
Society, 2026. https://doi.org/10.1103/rbg2-f61m.
ieee: M. Votto et al., “Learning mixed quantum states in large-scale experiments,”
Physical Review Letters, vol. 136, no. 9. American Physical Society, 2026.
ista: Votto M, Ljubotina M, Lancien C, Cirac JI, Zoller P, Serbyn M, Piroli L, Vermersch
B. 2026. Learning mixed quantum states in large-scale experiments. Physical Review
Letters. 136(9), 090801.
mla: Votto, Matteo, et al. “Learning Mixed Quantum States in Large-Scale Experiments.”
Physical Review Letters, vol. 136, no. 9, 090801, American Physical Society,
2026, doi:10.1103/rbg2-f61m.
short: M. Votto, M. Ljubotina, C. Lancien, J.I. Cirac, P. Zoller, M. Serbyn, L.
Piroli, B. Vermersch, Physical Review Letters 136 (2026).
date_created: 2026-03-23T14:56:32Z
date_published: 2026-03-04T00:00:00Z
date_updated: 2026-03-23T15:39:34Z
day: '04'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/rbg2-f61m
external_id:
arxiv:
- '2507.12550'
file:
- access_level: open_access
checksum: 12b16ce2d49c62b2909da95121bfaadb
content_type: application/pdf
creator: dernst
date_created: 2026-03-23T15:35:27Z
date_updated: 2026-03-23T15:35:27Z
file_id: '21491'
file_name: 2026_PhysicalReviewLetters_Votto.pdf
file_size: 500041
relation: main_file
success: 1
file_date_updated: 2026-03-23T15:35:27Z
has_accepted_license: '1'
intvolume: ' 136'
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Learning mixed quantum states in large-scale experiments
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: 136
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21482'
abstract:
- lang: eng
text: Controlling the size and shape of assembled structures is a fundamental challenge
in self-assembly and is highly relevant in material design and biology. Here,
we show that specific but promiscuous short-range binding interactions make it
possible to economically assemble linear filaments of user-defined length. Our
approach leads to independent control over the mean and width of the filament
size distribution and allows us to smoothly explore design trade-offs between
assembly quality (spread in size) and cost (number of particle species). We employ
a simple hierarchical assembly protocol to minimize assembly times and show that
multiple stages of hierarchy make it possible to extend our approach to the assembly
of higher-dimensional structures. Our work provides a conceptually simple solution
to size control that is applicable to a broad range of systems, from DNA nanoparticles
to supramolecular polymers and beyond.
acknowledgement: We thank Maitane Muñoz-Basagoiti for helpful discussions. The research
was supported by the Gesellschaft für Forschungsförderung Niederösterreich under
Project No. FTI23-G-011.
article_number: L012054
article_processing_charge: Yes
article_type: original
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. Physical
Review Research. 2026;8. doi:10.1103/68rs-3qgn
apa: Hübl, M., & Goodrich, C. P. (2026). Entropic size control of self-assembled
filaments. Physical Review Research. American Physical Society. https://doi.org/10.1103/68rs-3qgn
chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled
Filaments.” Physical Review Research. American Physical Society, 2026.
https://doi.org/10.1103/68rs-3qgn.
ieee: M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,”
Physical Review Research, vol. 8. American Physical Society, 2026.
ista: Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments.
Physical Review Research. 8, L012054.
mla: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled
Filaments.” Physical Review Research, vol. 8, L012054, American Physical
Society, 2026, doi:10.1103/68rs-3qgn.
short: M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026).
corr_author: '1'
date_created: 2026-03-23T14:58:31Z
date_published: 2026-03-05T00:00:00Z
date_updated: 2026-03-23T15:59:11Z
day: '05'
ddc:
- '530'
department:
- _id: CaGo
- _id: GradSch
doi: 10.1103/68rs-3qgn
file:
- access_level: open_access
checksum: 6d8a68e4a19f8dad5abdf75f72316f3d
content_type: application/pdf
creator: dernst
date_created: 2026-03-23T15:53:29Z
date_updated: 2026-03-23T15:53:29Z
file_id: '21493'
file_name: 2026_PhysicalReviewResearch_Huebl.pdf
file_size: 2680924
relation: main_file
success: 1
file_date_updated: 2026-03-23T15:53:29Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entropic size control of self-assembled filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21490'
abstract:
- lang: eng
text: Auxin canalization is a self-organizing process that governs the flexible
formation of vasculature by reinforcing the formation of auxin transport channels.
A key prerequisite is the feedback between auxin signaling and directional auxin
transport, mediated by PIN transporters. Despite the developmental importance
of canalization, the molecular components linking auxin perception to the regulation
of PIN auxin transporters remain poorly understood. Here, we identify TOW, a novel
and essential component of auxin canalization that links intracellular auxin signaling
with cell surface auxin perception. TOW is regulated downstream of TIR1/AFB-Aux/IAA-WRKY23
transcriptional auxin signaling. tow mutants exhibit defects in regeneration and
de novo vasculature formation, along with impaired formation of polarized, PIN-expressing
auxin channels. At the subcellular level, these mutants display disrupted auxin-induced
PIN polarization and altered PIN endocytic trafficking dynamics. TOW localizes
predominantly to the plasma membrane, where it interacts with receptor-like kinases
involved in auxin canalization, including the TMK1 auxin co-receptor and the CAMEL-CANAR
complex. TOW promotes PIN interaction with these kinases and stabilizes PINs at
the cell surface. Together, our findings identify TOW as a molecular link between
intracellular and cell surface auxin signaling mechanisms that converge on PIN
trafficking and polarity, providing new insights into how auxin signaling regulates
directional auxin transport for the self-organizing formation of vasculature during
flexible plant development.
acknowledged_ssus:
- _id: MassSpec
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Dr. Z. Ge (ISTA) for providing vectors for the CRISPR-Cas9
system, Dr. Armel Nicolas and Dr. Bella Bruszel for phosphoproteomic analysis, Prof.
Michael Wrzaczek (Czech Academy of Sciences, Czechia) for valuable suggestions,
and Prof. Maciek Adamowski (University of Gdańsk) for technical assistance. We also
acknowledge the support of the Mass Spectrometry and Proteomics Facility, the Imaging
& Optics Facility, and the Lab Support Facility at the Institute of Science and
Technology Austria. This research was supported by the Scientific Service Units
(SSU) of ISTA, utilizing resources provided by the Imaging & Optics Facility (IOF)
and the Lab Support Facility (LSF). The work conducted by the Friml group was funded
by the European Research Council (ERC) under grant agreement no. 101142681 (CYNIPS)
and by the Austrian Science Fund (FWF) under project ESP271. We acknowledge the
core facility CELLIM supported by MEYS CR (LM2023050 Czech-BioImaging) and the Plant
Sciences Core Facility of CEITEC Masaryk University. E.M. received support from
the National Science Centre (NCN), Poland, through the OPUS call within the Weave
programme (grant no. 2021/43/I/NZ1/01835). T.N. received support from TowArds Next
GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the ERDF Programme Johannes
Amos Comenius.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mingyue
full_name: Li, Mingyue
id: 01f96916-0235-11eb-9379-a323192643b7
last_name: Li
- first_name: Nikola
full_name: Rydza, Nikola
last_name: Rydza
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. Receptor-like-kinase-interacting
protein TOW stabilizes PIN transporters for auxin canalization. Current Biology.
2026;36(6):1468-1480.e6. doi:10.1016/j.cub.2026.02.023
apa: Li, M., Rydza, N., Mazur, E., Molnar, G., Nodzyński, T., & Friml, J. (2026).
Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin
canalization. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2026.02.023
chicago: Li, Mingyue, Nikola Rydza, Ewa Mazur, Gergely Molnar, Tomasz Nodzyński,
and Jiří Friml. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters
for Auxin Canalization.” Current Biology. Elsevier, 2026. https://doi.org/10.1016/j.cub.2026.02.023.
ieee: M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, and J. Friml, “Receptor-like-kinase-interacting
protein TOW stabilizes PIN transporters for auxin canalization,” Current Biology,
vol. 36, no. 6. Elsevier, p. 1468–1480.e6, 2026.
ista: Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. 2026. Receptor-like-kinase-interacting
protein TOW stabilizes PIN transporters for auxin canalization. Current Biology.
36(6), 1468–1480.e6.
mla: Li, Mingyue, et al. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes
PIN Transporters for Auxin Canalization.” Current Biology, vol. 36, no.
6, Elsevier, 2026, p. 1468–1480.e6, doi:10.1016/j.cub.2026.02.023.
short: M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, J. Friml, Current Biology
36 (2026) 1468–1480.e6.
corr_author: '1'
date_created: 2026-03-23T15:11:16Z
date_published: 2026-03-23T00:00:00Z
date_updated: 2026-03-24T08:36:40Z
day: '23'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cub.2026.02.023
external_id:
pmid:
- '41831441'
file:
- access_level: open_access
checksum: fe6c41fdab58a55df5f2a5860c02acdc
content_type: application/pdf
creator: dernst
date_created: 2026-03-24T08:34:37Z
date_updated: 2026-03-24T08:34:37Z
file_id: '21496'
file_name: 2026_CurrentBiology_Li.pdf
file_size: 12986894
relation: main_file
success: 1
file_date_updated: 2026-03-24T08:34:37Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1468-1480.e6
pmid: 1
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: bd906599-d553-11ed-ba76-abf8547645d7
grant_number: E271
name: Identification of a novel regulator in auxin canalization
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for
auxin canalization
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: 36
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21484'
abstract:
- lang: eng
text: An individual's phenotype reflects a complex interplay of the direct effects
of their DNA, epigenetic modifications of their DNA induced by their parents,
and indirect effects of their parents' DNA. Here, we derive how the genetic variance
within a population is changed under the influence of indirect maternal, paternal
and parent-of-origin effects under random mating. We also consider indirect effects
of a sibling, in particular how the genetic variance is altered when looking at
the phenotypic difference between two siblings. The calculations are then extended
to include assortative mating (AM), which alters the variance by inducing increased
homozygosity and correlations within and across loci. AM likely leads to covariance
of parental genetic effects, a measure of the similarity of parents in the indirect
effects they have on their children. We propose that this assortment for parental
characteristics, where biological parents create similar environments for their
children, can create shared parental effects across traits and the appearance
of cross-trait AM. Our theory shows how the resemblance among relatives increases
under both AM, indirect and parent-of-origin effects. When our model is used to
predict correlations among relatives in human height, we find that explaining
the patterns observed in real data requires both indirect genetic effects and
assortative mating. The degree to which direct, indirect and epigenetic effects
shape the phenotypic variance of complex traits remains an open question that
requires large-scale family data to be resolved.
acknowledgement: We thank members of the Medical Genomics group at ISTA for their
comments, which improved this manuscript. This work was funded by an SNSF Eccellenza
Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science
and Technology Austria.
article_number: iyag042
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ilse
full_name: Krätschmer, Ilse
id: 30d4014e-7753-11eb-b44b-db6d61112e73
last_name: Krätschmer
orcid: 0000-0002-5636-9259
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Krätschmer I, Robinson MR. A quantitative genetic model for indirect genetic
effects and genomic imprinting under random and assortative mating. Genetics.
2026. doi:10.1093/genetics/iyag042
apa: Krätschmer, I., & Robinson, M. R. (2026). A quantitative genetic model
for indirect genetic effects and genomic imprinting under random and assortative
mating. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyag042
chicago: Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic
Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative
Mating.” Genetics. Oxford University Press, 2026. https://doi.org/10.1093/genetics/iyag042.
ieee: I. Krätschmer and M. R. Robinson, “A quantitative genetic model for indirect
genetic effects and genomic imprinting under random and assortative mating,” Genetics.
Oxford University Press, 2026.
ista: Krätschmer I, Robinson MR. 2026. A quantitative genetic model for indirect
genetic effects and genomic imprinting under random and assortative mating. Genetics.,
iyag042.
mla: Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model
for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative
Mating.” Genetics, iyag042, Oxford University Press, 2026, doi:10.1093/genetics/iyag042.
short: I. Krätschmer, M.R. Robinson, Genetics (2026).
corr_author: '1'
date_created: 2026-03-23T15:02:54Z
date_published: 2026-02-12T00:00:00Z
date_updated: 2026-03-24T06:48:10Z
day: '12'
department:
- _id: MaRo
doi: 10.1093/genetics/iyag042
external_id:
pmid:
- '41677404'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/genetics/iyag042
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/medical-genomics-group/familyMC
status: public
title: A quantitative genetic model for indirect genetic effects and genomic imprinting
under random and assortative mating
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: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21486'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analyzed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find that
the majority of turnovers happened in the group Schizophora, which tend to have
fewer genes on Muller element F (the chromosome homologous to the ancestral insect
X chromosome) than lower dipterans, a factor previously hypothesized to facilitate
turnover. Most derived X chromosomes have higher GC content than autosomes, consistent
with a high prevalence of male achiasmy in Diptera. In addition, an excess of
gene movement out of the X is detected for most of these new X chromosomes, and
many of these moved genes have high testis expression in Drosophila, suggesting
that out-of-X gene movement contributes to the long-term demasculinization of
X chromosomes.
acknowledgement: This work was supported by a grant from the Austrian Science Fund
(FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback
on an early version of the manuscript. We are grateful to Kamil Jaron and Julia
Gries for helpful discussions and for sharing their unpublished work. Computational
resources and support were provided by the Scientific Computing Unit at ISTA.
article_number: qrag003
article_processing_charge: Yes
article_type: original
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters. 2026. doi:10.1093/evlett/qrag003
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Causes and consequences
of sex-chromosome turnovers in Diptera. Evolution Letters. Oxford University
Press. https://doi.org/10.1093/evlett/qrag003
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Evolution Letters.
Oxford University Press, 2026. https://doi.org/10.1093/evlett/qrag003.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera,” Evolution Letters. Oxford University
Press, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters., qrag003.
mla: Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome
Turnovers in Diptera.” Evolution Letters, qrag003, Oxford University Press,
2026, doi:10.1093/evlett/qrag003.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026).
corr_author: '1'
date_created: 2026-03-23T15:05:42Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-03-24T07:14:08Z
day: '12'
ddc:
- '570'
department:
- _id: BeVi
- _id: GradSch
doi: 10.1093/evlett/qrag003
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
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month: '03'
oa: 1
oa_version: Published Version
project:
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grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Causes and consequences of sex-chromosome turnovers in Diptera
tmp:
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short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
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acknowledged_ssus:
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- _id: EM-Fac
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
citation:
ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
- contributor_type: researcher
first_name: Yann-Edwin
last_name: Keta
- contributor_type: supervisor
first_name: 'Silke '
last_name: Henkes
- contributor_type: supervisor
first_name: Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- contributor_type: supervisor
first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
corr_author: '1'
date_created: 2026-02-04T16:38:02Z
date_published: 2026-03-24T00:00:00Z
date_updated: 2026-03-24T08:32:00Z
day: '24'
department:
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- _id: CaHe
- _id: EdHa
doi: 10.15479/AT-ISTA-21137
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creator: snaik
date_created: 2026-03-16T11:51:10Z
date_updated: 2026-03-16T11:51:10Z
description: 'Python3 library written in C++20 to integrate vertex models. Please
read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed
instructions for installation and usage of the code in this repository. '
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license: https://creativecommons.org/licenses/by-sa/4.0/
month: '3'
oa: 1
oa_version: None
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
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legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
_id: '21489'
abstract:
- lang: eng
text: We study Kirillov algebras attached to minuscule highest weight representations
of semisimple Lie algebras. They can be viewed as equivariant cohomology algebras
of partial flag varieties. Real structures on the varieties then induce involutions
of these algebras. We describe how these involutions act on the spectra of minuscule
Kirillov algebras, and model the fixed points via the equivariant cohomology of
real partial flag varieties. We then use this model to characterise freeness of
the fixed point coordinate ring over the appropriate base. As an application,
we recover a q = -1 phenomenon of Stembridge in the minuscule case by geometric
means.
acknowledgement: 'I would like to thank Tamás Hausel for introducing me to this area
of mathematics and for his constant guidance. I would also like to thank Jakub Löwit
and Miguel González for fruitful discussions and many helpful comments on this paper.
This work was done during the author’s PhD studies at the Institute of Science and
Technology Austria (ISTA). It was funded by the Austrian Science Fund (FWF) 10.55776/P35847.
Open access funding provided by Institute of Science and Technology (IST Austria). '
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- first_name: Mischa M
full_name: Elkner, Mischa M
id: 477faa59-080d-11ed-979a-c693ab7638ab
last_name: Elkner
citation:
ama: Elkner MM. On involutions of minuscule Kirillov algebras induced by real structures.
Transformation Groups. 2026. doi:10.1007/s00031-026-09958-y
apa: Elkner, M. M. (2026). On involutions of minuscule Kirillov algebras induced
by real structures. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-026-09958-y
chicago: Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced
by Real Structures.” Transformation Groups. Springer Nature, 2026. https://doi.org/10.1007/s00031-026-09958-y.
ieee: M. M. Elkner, “On involutions of minuscule Kirillov algebras induced by real
structures,” Transformation Groups. Springer Nature, 2026.
ista: Elkner MM. 2026. On involutions of minuscule Kirillov algebras induced by
real structures. Transformation Groups.
mla: Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by
Real Structures.” Transformation Groups, Springer Nature, 2026, doi:10.1007/s00031-026-09958-y.
short: M.M. Elkner, Transformation Groups (2026).
corr_author: '1'
date_created: 2026-03-23T15:10:43Z
date_published: 2026-03-14T00:00:00Z
date_updated: 2026-03-24T08:26:10Z
day: '14'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1007/s00031-026-09958-y
external_id:
arxiv:
- '2411.16270'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1007/s00031-026-09958-y
month: '03'
oa: 1
oa_version: None
project:
- _id: 34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3
grant_number: P35847
name: Geometry of the tip of the global nilpotent cone
publication: Transformation Groups
publication_identifier:
eissn:
- 1531-586X
issn:
- 1083-4362
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On involutions of minuscule Kirillov algebras induced by real structures
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: '2026'
...
---
OA_place: repository
_id: '21393'
abstract:
- lang: eng
text: "This thesis documents a voyage towards truth and beauty via formal verification
of theorems. To this end, we develop libraries in Lean 4 that present definitions
and results from diverse areas of MathematiCS (i.e., Mathematics and Computer
Science). The aim is to create code that is understandable, believable, useful,
and elegant. The code should stand for itself as much as possible without a need
for documentation; however, this text redundantly documents our code artifacts
and provides additional context that isn’t present in the code. This thesis is
written for readers who know Lean 4 but are not familiar with any of the topics
presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe
formalize general grammars in Lean 4 and use grammars to show closure of the class
of type-0 languages under four operations; union, reversal, concatenation, and
the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas
established that a system of linear inequalities has a solution if and only if
we cannot obtain a contradiction by taking a linear combination of the inequalities.
We state and formally prove several Farkas-like theorems over linearly ordered
fields in Lean 4. Furthermore, we extend duality theory to the case when some
coefficients are allowed to take “infinite values”. Additionally, we develop the
basics of the theory of optimization in terms of the framework called General-Valued
Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint
Satisfaction Problem template has symmetric fractional polymorphisms of all arities,
then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory.
Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting
a structural characterization of the class of regular matroids. We aim to formally
verify Seymour’s theorem in Lean 4. First, we build a library for working with
totally unimodular matrices. We define binary matroids and their standard representations,
and we prove that they form a matroid in the sense how Mathlib defines matroids.
We define regular matroids to be matroids for which there exists a full representation
rational matrix that is totally unimodular, and we prove that all regular matroids
are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways
to compose their standard representation matrices. We prove that the 1-sum, the
2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes
the composition direction of the Seymour’s theorem. The (more difficult) decomposition
direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying
the trusted code in each project and presenting it faithfully. We emphasize the
readability and believability of definitions rather than choosing definitions
that are easier to work with. In search for beauty, we focus on the philosophical
framework of Roger Scruton, who emphasizes that beauty is not a mere decoration
but, most importantly, beauty is the means for shaping our place in the world
and a source of redemption, where it can be viewed as a substitute for religion."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
citation:
ama: 'Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory
of grammars, optimization, matroids. 2026. doi:10.15479/AT-ISTA-21393'
apa: 'Dvorak, M. (2026). Pursuit of truth and beauty in Lean 4 : Formally verified
theory of grammars, optimization, matroids. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-21393'
chicago: 'Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified
Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-21393.'
ieee: 'M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory
of grammars, optimization, matroids,” Institute of Science and Technology Austria,
2026.'
ista: 'Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified
theory of grammars, optimization, matroids. Institute of Science and Technology
Austria.'
mla: 'Dvorak, Martin. Pursuit of Truth and Beauty in Lean 4 : Formally Verified
Theory of Grammars, Optimization, Matroids. Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21393.'
short: 'M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory
of Grammars, Optimization, Matroids, Institute of Science and Technology Austria,
2026.'
corr_author: '1'
date_created: 2026-03-04T09:26:46Z
date_published: 2026-03-04T00:00:00Z
date_updated: 2026-03-27T12:37:00Z
day: '04'
ddc:
- '511'
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: VlKo
doi: 10.15479/AT-ISTA-21393
file:
- access_level: open_access
checksum: cface6dc18152680962b5361575f6e4f
content_type: application/pdf
creator: mdvorak
date_created: 2026-03-04T08:56:15Z
date_updated: 2026-03-04T08:56:15Z
file_id: '21394'
file_name: 2026_Dvorak_Martin_Thesis.pdf
file_size: 1771231
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creator: mdvorak
date_created: 2026-03-04T09:03:37Z
date_updated: 2026-03-04T09:03:37Z
file_id: '21395'
file_name: 2026_Dvorak_Martin_Thesis.docx
file_size: 864585
relation: source_file
file_date_updated: 2026-03-04T09:03:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '160'
publication_identifier:
isbn:
- 978-3-99078-074-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
link:
- description: Full version of all definitions, statements, and proofs for Chapter
3.1 (Linear duality)
relation: software
url: https://github.com/madvorak/duality/tree/v3.5.0
- description: Full version of all definitions, statements, and proofs for Chapter
3.2 (Valued Constraint Satisfaction Problems)
relation: software
url: https://github.com/madvorak/vcsp/tree/v8.2.0
- description: Full version of all definitions, statements, and proofs for Chapter
4 (Seymour project)
relation: software
url: https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0
- description: Full version of all definitions, statements, and proofs for Chapter
5 (Theory of grammars)
relation: software
url: https://github.com/madvorak/chomsky/tree/v1.2.0
- description: Old version (Lean 3) of the project about grammars
relation: software
url: https://github.com/madvorak/grammars
- description: Demonstration of (minimal) requirements for selected algebraic classes
used in my Ph.D. thesis
relation: software
url: https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean
record:
- id: '13120'
relation: part_of_dissertation
status: public
- id: '21398'
relation: part_of_dissertation
status: public
- id: '20071'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Jasmin
full_name: Blanchette, Jasmin
last_name: Blanchette
title: 'Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars,
optimization, matroids'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21501'
abstract:
- lang: eng
text: "Kinetically constrained models were originally introduced to capture slow
relaxation in glassy systems, where dynamics are hindered by local constraints
instead of energy barriers. Their quantum counterparts have recently drawn attention
for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming
from chiral symmetry. Yet, the structure and implications of these zero modes
remain poorly understood. In this work, we focus on the properties of the zero
mode subspace in quantum kinetically constrained models with a U(1) particle-conservation
symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric
U(1) East-West models to illustrate our two main results. First, we observe that
the simultaneous presence of constraints and chiral symmetry generally leads to
a parametric increase in the number of zero modes due to the fragmentation of
the many-body\r\nHilbert space into disconnected sectors. Second, we generalize
the concept of compact localized states from single-particle physics and introduce
the notion of collective bound states, a special kind of nonergodic eigenstates
that are robust to enlarging the system size. We formulate sufficient criteria
for their existence, arguing that the degenerate zero mode subspace plays a central
role, and demonstrate bound states in both example models and in a two-dimensional
model, the U(1) North-East, and in the pairflip model, a system without particle
conservation. Our results motivate a systematic study of bound states and their
relation to ergodicity breaking, transport, and other properties of quantum kinetically
constrained\r\nmodels. "
acknowledgement: The authors acknowledge useful discussions with Berislav Buca. This
work was supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L.
acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research
was supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical
Physics (KITP).
article_number: '010352'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Eulalia
full_name: Nicolau Jimenez, Eulalia
id: 04b4791c-8fd7-11ee-a7df-be2fdc569c48
last_name: Nicolau Jimenez
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Nicolau Jimenez E, Ljubotina M, Serbyn M. Fragmentation, zero modes, and collective
bound states in constrained models. PRX Quantum. 2026;7. doi:10.1103/sl79-1xgb
apa: Nicolau Jimenez, E., Ljubotina, M., & Serbyn, M. (2026). Fragmentation,
zero modes, and collective bound states in constrained models. PRX Quantum.
American Physical Society. https://doi.org/10.1103/sl79-1xgb
chicago: Nicolau Jimenez, Eulalia, Marko Ljubotina, and Maksym Serbyn. “Fragmentation,
Zero Modes, and Collective Bound States in Constrained Models.” PRX Quantum.
American Physical Society, 2026. https://doi.org/10.1103/sl79-1xgb.
ieee: E. Nicolau Jimenez, M. Ljubotina, and M. Serbyn, “Fragmentation, zero modes,
and collective bound states in constrained models,” PRX Quantum, vol. 7.
American Physical Society, 2026.
ista: Nicolau Jimenez E, Ljubotina M, Serbyn M. 2026. Fragmentation, zero modes,
and collective bound states in constrained models. PRX Quantum. 7, 010352.
mla: Nicolau Jimenez, Eulalia, et al. “Fragmentation, Zero Modes, and Collective
Bound States in Constrained Models.” PRX Quantum, vol. 7, 010352, American
Physical Society, 2026, doi:10.1103/sl79-1xgb.
short: E. Nicolau Jimenez, M. Ljubotina, M. Serbyn, PRX Quantum 7 (2026).
corr_author: '1'
date_created: 2026-03-28T14:57:56Z
date_published: 2026-03-13T00:00:00Z
date_updated: 2026-03-30T06:09:28Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/sl79-1xgb
ec_funded: 1
external_id:
arxiv:
- '2504.17627'
file:
- access_level: open_access
checksum: d155ffa9e1a8275702149165f4bf963c
content_type: application/pdf
creator: dernst
date_created: 2026-03-30T06:08:07Z
date_updated: 2026-03-30T06:08:07Z
file_id: '21505'
file_name: 2026_PRXQuantum_Nicolau.pdf
file_size: 1848724
relation: main_file
success: 1
file_date_updated: 2026-03-30T06:08:07Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fragmentation, zero modes, and collective bound states in constrained models
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: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '21503'
abstract:
- lang: eng
text: Currently, pharmacogenetics relies on partially annotated star alleles, leaving
novel variants and complex haplotypes uninterpretable. Computational scoring frameworks
could overcome these limitations. Here, we comprehensively evaluated the ability
of existing (CADD, FATHMM-XF, PROVEAN, MutationAssessor, SIFT, PhyloP100, APF,
APF2) and novel (PharmGScore and PharmMLScore) variant effect predictors to assess
pharmacogenetic alleles in multiple scenarios. Altogether we analyzed 541 PharmVar
alleles, high‑throughput CYP2C9 and CYP2C19 mutational maps, and 200 642 UK Biobank
exomes linked with health records containing antidepressant treatment outcomes.
Many evaluated tools, especially ensemble frameworks, matched or exceeded star
allele classifications (ROC‑AUC up to 0.85 for allele definitions, 0.95 in vitro;
TPR up to 0.99 for exomes) and accurately predicted severe antidepressant adverse
events for carriers of deleterious variants in CYP2C19 (OR 1.20–1.35). Our findings
show that computational predictors deliver star allele accuracy while overcoming
their limitations. With additional validation, computational tools could enhance
clinical decision frameworks by enabling continuous scoring, incorporating previously
unknown variants, and providing genome-wide applicability.
acknowledgement: "This research has been conducted using the UK Biobank Resource under
Application Number 62979. We are grateful to the UK Biobank and all its voluntary
participants. This work used data provided by patients and collected by the NHS
as part of their care and support.\r\n\r\nThis study was funded by the National
Science Center, Poland: PRELUDIUM BIS-3 grant no. 2021/43/O/NZ7/01187 (development
and benchmarking of variant scores) and SONATINA 5 grant 2021/40/C/NZ2/00218 (UKB
analyses). Additional support came from the statutory funds of the Maj Institute
of Pharmacology PAS. We gratefully acknowledge Poland’s high-performance Infrastructure
PLGrid ACK Cyfronet AGH, for providing computer facilities and support within computational
grant no PLG/2022/015861. DMF and GEB were funded by NIH grants NIH R35GM152106
and UM1HG011969."
article_number: '8'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jacek
full_name: Hajto, Jacek
last_name: Hajto
- first_name: Marcin
full_name: Piechota, Marcin
last_name: Piechota
- first_name: Ilse
full_name: Krätschmer, Ilse
id: 30d4014e-7753-11eb-b44b-db6d61112e73
last_name: Krätschmer
orcid: 0000-0002-5636-9259
- first_name: Paula
full_name: Konowalska, Paula
last_name: Konowalska
- first_name: Gabriel E.
full_name: Boyle, Gabriel E.
last_name: Boyle
- first_name: Douglas M.
full_name: Fowler, Douglas M.
last_name: Fowler
- first_name: Malgorzata
full_name: Borczyk, Malgorzata
last_name: Borczyk
- first_name: Michal
full_name: Korostynski, Michal
last_name: Korostynski
citation:
ama: 'Hajto J, Piechota M, Krätschmer I, et al. Computational variant predictors
for pharmacogenomics: From evaluation of single alleles to assessment of adverse
drug reactions to antidepressants. Pharmacogenomics Journal. 2026;26(2).
doi:10.1038/s41397-026-00399-0'
apa: 'Hajto, J., Piechota, M., Krätschmer, I., Konowalska, P., Boyle, G. E., Fowler,
D. M., … Korostynski, M. (2026). Computational variant predictors for pharmacogenomics:
From evaluation of single alleles to assessment of adverse drug reactions to antidepressants.
Pharmacogenomics Journal. Springer Nature. https://doi.org/10.1038/s41397-026-00399-0'
chicago: 'Hajto, Jacek, Marcin Piechota, Ilse Krätschmer, Paula Konowalska, Gabriel
E. Boyle, Douglas M. Fowler, Malgorzata Borczyk, and Michal Korostynski. “Computational
Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to
Assessment of Adverse Drug Reactions to Antidepressants.” Pharmacogenomics
Journal. Springer Nature, 2026. https://doi.org/10.1038/s41397-026-00399-0.'
ieee: 'J. Hajto et al., “Computational variant predictors for pharmacogenomics:
From evaluation of single alleles to assessment of adverse drug reactions to antidepressants,”
Pharmacogenomics Journal, vol. 26, no. 2. Springer Nature, 2026.'
ista: 'Hajto J, Piechota M, Krätschmer I, Konowalska P, Boyle GE, Fowler DM, Borczyk
M, Korostynski M. 2026. Computational variant predictors for pharmacogenomics:
From evaluation of single alleles to assessment of adverse drug reactions to antidepressants.
Pharmacogenomics Journal. 26(2), 8.'
mla: 'Hajto, Jacek, et al. “Computational Variant Predictors for Pharmacogenomics:
From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.”
Pharmacogenomics Journal, vol. 26, no. 2, 8, Springer Nature, 2026, doi:10.1038/s41397-026-00399-0.'
short: J. Hajto, M. Piechota, I. Krätschmer, P. Konowalska, G.E. Boyle, D.M. Fowler,
M. Borczyk, M. Korostynski, Pharmacogenomics Journal 26 (2026).
date_created: 2026-03-29T22:07:08Z
date_published: 2026-03-09T00:00:00Z
date_updated: 2026-03-30T07:10:50Z
day: '09'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1038/s41397-026-00399-0
external_id:
pmid:
- '41803106'
file:
- access_level: open_access
checksum: 2fd3d7e48b779ac24245f6c35449b89a
content_type: application/pdf
creator: dernst
date_created: 2026-03-30T07:04:08Z
date_updated: 2026-03-30T07:04:08Z
file_id: '21506'
file_name: 2026_PharmacogenomicsJour_Hajto.pdf
file_size: 2618963
relation: main_file
success: 1
file_date_updated: 2026-03-30T07:04:08Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Pharmacogenomics Journal
publication_identifier:
eissn:
- 1473-1150
issn:
- ' 1470-269X'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Computational variant predictors for pharmacogenomics: From evaluation of
single alleles to assessment of adverse drug reactions to antidepressants'
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: 26
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21509'
abstract:
- lang: eng
text: Chromatin remodeling complexes mobilize nucleosomes and promote transcription
factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron
microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2
and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages
TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler
ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without
structural interference. However, continued DNA translocation is expected to cause
collisions with bound TFs, which can trigger remodeling direction reversals or
may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes
structural rearrangements, and ensemble assays reveal a nucleosome subpopulation
translocating away from TF-binding sites. Moreover, single-molecule experiments
show that nucleosome-bound BAF frequently changes remodeling direction, and we
identify an ADP-bound remodeler conformation as a potential intermediate. Together,
these findings reveal key aspects of the conformational dynamics and remodeling
outcomes underlying BAF processing of TF-bound nucleosomes.
acknowledgement: We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics
and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada,
D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance
for critical discussions; and members of the Thomä lab for helpful feedback. Support
for this work was provided to N.H.T. by the European Research Council under the
European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis
Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852,
and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and
KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS,
no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden
(25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported
by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported
by an EMBO fellowship (ALTF 549-2021).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Luca
full_name: Vecchia, Luca
last_name: Vecchia
- first_name: David
full_name: Domjan, David
last_name: Domjan
- first_name: Simone
full_name: Cavadini, Simone
last_name: Cavadini
- first_name: Anton
full_name: Sabantsev, Anton
last_name: Sabantsev
- first_name: Georg
full_name: Kempf, Georg
last_name: Kempf
- first_name: Ganesh R.
full_name: Pathare, Ganesh R.
last_name: Pathare
- first_name: Klaus
full_name: Brackmann, Klaus
last_name: Brackmann
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Lukas
full_name: Kater, Lukas
last_name: Kater
- first_name: Eric
full_name: Hietter-Pfeiffer, Eric
last_name: Hietter-Pfeiffer
- first_name: Mina
full_name: Haddawi, Mina
last_name: Haddawi
- first_name: Urja P.
full_name: Kuber, Urja P.
last_name: Kuber
- first_name: Sandra
full_name: Mühlhäusser, Sandra
last_name: Mühlhäusser
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Michael B.
full_name: Stadler, Michael B.
last_name: Stadler
- first_name: Sebastian
full_name: Deindl, Sebastian
last_name: Deindl
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes
nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell.
2026;86(4):625-639.e8. doi:10.1016/j.molcel.2026.01.021
apa: Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G.,
… Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes
bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. Elsevier.
https://doi.org/10.1016/j.molcel.2026.01.021
chicago: Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev,
Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes
Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell.
Elsevier, 2026. https://doi.org/10.1016/j.molcel.2026.01.021.
ieee: J. Weiss et al., “The human BAF chromatin remodeler processes nucleosomes
bound by pioneer transcription factors OCT4–SOX2,” Molecular Cell, vol.
86, no. 4. Elsevier, p. 625–639.e8, 2026.
ista: Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR,
Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser
S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler
processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular
Cell. 86(4), 625–639.e8.
mla: Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes
Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell, vol.
86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:10.1016/j.molcel.2026.01.021.
short: J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R.
Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi,
U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular
Cell 86 (2026) 625–639.e8.
date_created: 2026-03-30T11:58:48Z
date_published: 2026-02-19T00:00:00Z
date_updated: 2026-03-30T12:09:08Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2026.01.021
external_id:
pmid:
- '41679301'
file:
- access_level: open_access
checksum: e16a7315b64a706184b177ea1621523c
content_type: application/pdf
creator: dernst
date_created: 2026-03-30T12:04:38Z
date_updated: 2026-03-30T12:04:38Z
file_id: '21510'
file_name: 2026_MolecularCell_Weiss.pdf
file_size: 9786677
relation: main_file
success: 1
file_date_updated: 2026-03-30T12:04:38Z
has_accepted_license: '1'
intvolume: ' 86'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 625-639.e8
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription
factors OCT4–SOX2
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: 86
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21483'
abstract:
- lang: eng
text: 'Embryogenesis in the model plant Arabidopsis thaliana provides a framework
for understanding how cell polarity and patterning coordinate with hormonal signalling
to establish the plant body plan. Following fertilisation, the zygote divides
asymmetrically to generate apical and basal lineages, establishing the apical–basal
axis that defines future shoot and root poles. Genetic and molecular analyses
of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless
revealed that localised auxin biosynthesis, directional transport and downstream
transcriptional responses are central to apical–basal axis establishment and organ
initiation. The main components of this regulation are polarly localised PIN auxin
transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX
transcription factors. Advances in microscopy have transformed the study of Arabidopsis
embryogenesis: fluorescence-compatible clearing reagents and three-dimensional
reconstructions now permit quantitative analyses of cell geometry, division orientation,
and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning
and multiphoton microscopes enable real-time observation of embryo development,
while laser-assisted cell ablation can be used to probe cell-to-cell communication
and fate plasticity. Together, these methodological breakthroughs position Arabidopsis
embryos as a prime model for dissecting the chemical and biophysical cues that
shape plant development.'
acknowledgement: The authors would like to acknowledge the many colleagues whose valuable
contributions to the field could not be included in this review due to space limitations
and reference constraints. Open Access funding provided by Institute of Science
and Technology Austria/KEMÖ.
article_number: nph.71072
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: David
full_name: Babic, David
id: db566d23-f6e0-11ea-865d-e6f270e968e7
last_name: Babic
- first_name: Milan
full_name: Zupunski, Milan
id: f6a21fce-573e-11f0-a150-a8d96aee2539
last_name: Zupunski
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Babic D, Zupunski M, Friml J. Imaging and genetic toolbox to study Arabidopsis
embryogenesis. New Phytologist. 2026. doi:10.1111/nph.71072
apa: Babic, D., Zupunski, M., & Friml, J. (2026). Imaging and genetic toolbox
to study Arabidopsis embryogenesis. New Phytologist. Wiley. https://doi.org/10.1111/nph.71072
chicago: Babic, David, Milan Zupunski, and Jiří Friml. “Imaging and Genetic Toolbox
to Study Arabidopsis Embryogenesis.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71072.
ieee: D. Babic, M. Zupunski, and J. Friml, “Imaging and genetic toolbox to study
Arabidopsis embryogenesis,” New Phytologist. Wiley, 2026.
ista: Babic D, Zupunski M, Friml J. 2026. Imaging and genetic toolbox to study Arabidopsis
embryogenesis. New Phytologist., nph. 71072.
mla: Babic, David, et al. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.”
New Phytologist, nph. 71072, Wiley, 2026, doi:10.1111/nph.71072.
short: D. Babic, M. Zupunski, J. Friml, New Phytologist (2026).
corr_author: '1'
date_created: 2026-03-23T14:59:06Z
date_published: 2026-03-11T00:00:00Z
date_updated: 2026-03-30T05:58:35Z
day: '11'
department:
- _id: JiFr
- _id: GradSch
doi: 10.1111/nph.71072
external_id:
pmid:
- '41808651'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.71072
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
status: public
title: Imaging and genetic toolbox to study Arabidopsis embryogenesis
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: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21502'
abstract:
- lang: eng
text: The mammalian brain stores glucose, the main circulating energy substrate,
as glycogen. In rodents, the cerebellum contains relatively high glycogen levels,
yet its cellular and subcellular distribution remains poorly defined. Using monoclonal
antibodies against glycogen, we examined its distribution in the mouse cerebellar
cortex. Glycogen was predominantly localized to Bergmann glia (BG) processes in
the molecular layer and was also detected in Purkinje cells (PCs), the principal
cerebellar neurons. To assess the functional significance of cerebellar glycogen,
we analyzed behavior in mice lacking glycogen synthase 1 (Gys1) in BG or PCs using
a floxed Gys1 line. Gys1 deficiency in either PCs or GFAP-positive cells reduced
anxiety-like behavior, whereas combined deletion caused PC degeneration and ataxia.
These findings reveal a critical role for glycogen metabolism in both astrocytes
and neurons in cerebellar function.
acknowledgement: This work was supported by the Novo Nordisk Foundation (NNFOC0058058,
H. Hirase), the Danmarks Frie Forskningsfond (0134-00107B and 5283-00069A, H.Hirase),
the Lundbeck Foundation, Japan Society for the Promotion of Science Grants-in-Aid
for Scientific Research (KAKENHI) program (22K06454/24H01221, A.K.; 23K27482, H.Hirai),
the Japan Agency for Medical Research and Development (AMED) Brain Mapping by Integrated
Neurotechnologies for Disease Studies (Brain/MINDS) (JP21dm0207111, H. Hirai), AMED
Brain/MINDS 2.0 (JP23wm0625001 and JP24wm0625103, H. Hirai), and grants from the
Spanish Ministerio de Ciencia e Innovación (MCIU/FEDER/AEI) (PID2020-118699 GB-100,
J.D.) and the Fundación Ramón Areces (J.D.). Sonam Akther has been supported by
the RIKEN IPA fellowship. We are thankful to Dr. Yuki Oe for his support in the
initial stage of this study and to Dan Xue for his help with the graphical abstract.
We thank Dr. Pia Weikop for providing CTN research infrastructure. The authors declare
no competing financial interests.
article_number: '115192'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sonam
full_name: Akther, Sonam
last_name: Akther
- first_name: Ashley Bomin
full_name: Lee, Ashley Bomin
last_name: Lee
- first_name: Ayumu
full_name: Konno, Ayumu
last_name: Konno
- first_name: Antonis
full_name: Asiminas, Antonis
last_name: Asiminas
- first_name: Marta
full_name: Vittani, Marta
last_name: Vittani
- first_name: Tsuneko
full_name: Mishima, Tsuneko
last_name: Mishima
- first_name: Hirokazu
full_name: Hirai, Hirokazu
last_name: Hirai
- first_name: Claire Francesca
full_name: Meehan, Claire Francesca
last_name: Meehan
- first_name: Jordi
full_name: Duran, Jordi
last_name: Duran
- first_name: Joan
full_name: Guinovart, Joan
last_name: Guinovart
- first_name: Hitoshi
full_name: Ashida, Hitoshi
last_name: Ashida
- first_name: Tsuyoshi
full_name: Morita, Tsuyoshi
last_name: Morita
- first_name: Otto
full_name: Baba, Otto
last_name: Baba
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Maiken
full_name: Nedergaard, Maiken
last_name: Nedergaard
- first_name: Hajime
full_name: Hirase, Hajime
last_name: Hirase
citation:
ama: Akther S, Lee AB, Konno A, et al. Distribution and functional significance
of rodent cerebellar glycogen. iScience. 2026;29(4). doi:10.1016/j.isci.2026.115192
apa: Akther, S., Lee, A. B., Konno, A., Asiminas, A., Vittani, M., Mishima, T.,
… Hirase, H. (2026). Distribution and functional significance of rodent cerebellar
glycogen. IScience. Elsevier. https://doi.org/10.1016/j.isci.2026.115192
chicago: Akther, Sonam, Ashley Bomin Lee, Ayumu Konno, Antonis Asiminas, Marta Vittani,
Tsuneko Mishima, Hirokazu Hirai, et al. “Distribution and Functional Significance
of Rodent Cerebellar Glycogen.” IScience. Elsevier, 2026. https://doi.org/10.1016/j.isci.2026.115192.
ieee: S. Akther et al., “Distribution and functional significance of rodent
cerebellar glycogen,” iScience, vol. 29, no. 4. Elsevier, 2026.
ista: Akther S, Lee AB, Konno A, Asiminas A, Vittani M, Mishima T, Hirai H, Meehan
CF, Duran J, Guinovart J, Ashida H, Morita T, Baba O, Shigemoto R, Nedergaard
M, Hirase H. 2026. Distribution and functional significance of rodent cerebellar
glycogen. iScience. 29(4), 115192.
mla: Akther, Sonam, et al. “Distribution and Functional Significance of Rodent Cerebellar
Glycogen.” IScience, vol. 29, no. 4, 115192, Elsevier, 2026, doi:10.1016/j.isci.2026.115192.
short: S. Akther, A.B. Lee, A. Konno, A. Asiminas, M. Vittani, T. Mishima, H. Hirai,
C.F. Meehan, J. Duran, J. Guinovart, H. Ashida, T. Morita, O. Baba, R. Shigemoto,
M. Nedergaard, H. Hirase, IScience 29 (2026).
date_created: 2026-03-29T22:07:07Z
date_published: 2026-03-17T00:00:00Z
date_updated: 2026-03-30T06:20:06Z
day: '17'
department:
- _id: RySh
doi: 10.1016/j.isci.2026.115192
external_id:
pmid:
- '41890976'
intvolume: ' 29'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.isci.2026.115192
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distribution and functional significance of rodent cerebellar glycogen
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21504'
abstract:
- lang: eng
text: Selecting an appropriate divergence measure is a critical aspect of machine
learning, as it directly impacts model performance. Among the most widely used,
we find the Kullback–Leibler (KL) divergence, originally introduced in kinetic
theory as a measure of relative entropy between probability distributions. Just
as in machine learning, the ability to quantify the proximity of probability distributions
plays a central role in kinetic theory. In this paper, we present a comparative
review of divergence measures rooted in kinetic theory, highlighting their theoretical
foundations and exploring their potential applications in machine learning and
artificial intelligence.
acknowledgement: "This work has been written within the activities of GNCS and GNFM
groups of INdAM (Italian\r\nNational Institute of High Mathematics). G.B. has been
funded by the European Union’s Horizon 2020 research and innovation programme under
the Marie Sklodowska-Curie grant agreement No 101034413. P.G. has been funded by
the European Union - NextGenerationEU, in the framework of the GRINSGrowing Resilient,
INclusive and Sustainable (GRINS PE00000018)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gennaro
full_name: Auricchio, Gennaro
last_name: Auricchio
- first_name: Giovanni
full_name: Brigati, Giovanni
id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1
last_name: Brigati
- first_name: Paolo
full_name: Giudici, Paolo
last_name: Giudici
- first_name: Giuseppe
full_name: Toscani, Giuseppe
last_name: Toscani
citation:
ama: 'Auricchio G, Brigati G, Giudici P, Toscani G. From kinetic theory to AI: A
rediscovery of high-dimensional divergences and their properties. Mathematical
Models and Methods in Applied Sciences. 2026. doi:10.1142/S0218202526410010'
apa: 'Auricchio, G., Brigati, G., Giudici, P., & Toscani, G. (2026). From kinetic
theory to AI: A rediscovery of high-dimensional divergences and their properties.
Mathematical Models and Methods in Applied Sciences. World Scientific Publishing.
https://doi.org/10.1142/S0218202526410010'
chicago: 'Auricchio, Gennaro, Giovanni Brigati, Paolo Giudici, and Giuseppe Toscani.
“From Kinetic Theory to AI: A Rediscovery of High-Dimensional Divergences and
Their Properties.” Mathematical Models and Methods in Applied Sciences.
World Scientific Publishing, 2026. https://doi.org/10.1142/S0218202526410010.'
ieee: 'G. Auricchio, G. Brigati, P. Giudici, and G. Toscani, “From kinetic theory
to AI: A rediscovery of high-dimensional divergences and their properties,” Mathematical
Models and Methods in Applied Sciences. World Scientific Publishing, 2026.'
ista: 'Auricchio G, Brigati G, Giudici P, Toscani G. 2026. From kinetic theory to
AI: A rediscovery of high-dimensional divergences and their properties. Mathematical
Models and Methods in Applied Sciences.'
mla: 'Auricchio, Gennaro, et al. “From Kinetic Theory to AI: A Rediscovery of High-Dimensional
Divergences and Their Properties.” Mathematical Models and Methods in Applied
Sciences, World Scientific Publishing, 2026, doi:10.1142/S0218202526410010.'
short: G. Auricchio, G. Brigati, P. Giudici, G. Toscani, Mathematical Models and
Methods in Applied Sciences (2026).
date_created: 2026-03-29T22:07:08Z
date_published: 2026-03-14T00:00:00Z
date_updated: 2026-03-30T06:56:35Z
day: '14'
department:
- _id: JaMa
doi: 10.1142/S0218202526410010
ec_funded: 1
external_id:
arxiv:
- '2507.11387'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.11387
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Mathematical Models and Methods in Applied Sciences
publication_identifier:
eissn:
- 1793-6314
issn:
- 0218-2025
publication_status: epub_ahead
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From kinetic theory to AI: A rediscovery of high-dimensional divergences and
their properties'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20865'
abstract:
- lang: eng
text: "We prove the convergence of a modified Jordan–Kinderlehrer–Otto scheme to
a solution\r\nto the Fokker–Planck equation in Ω e R^d with general—strictly positive
and temporally\r\nconstant—Dirichlet boundary conditions. We work under mild assumptions
on the domain,\r\nthe drift, and the initial datum. In the special case where
Ω is an interval in R1, we prove\r\nthat such a solution is a gradient flow—curve
of maximal slope—within a suitable space of\r\nmeasures, endowed with a modified
Wasserstein distance. Our discrete scheme and modified\r\ndistance draw inspiration
from contributions by A. Figalli and N. Gigli [J. Math. Pures\r\nAppl. 94, (2010),
pp. 107–130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41–88]\r\non
an optimal-transport approach to evolution equations with Dirichlet boundary conditions.\r\nSimilarly
to these works, we allow the mass to flow from/to the boundary ∂Ω throughout\r\nthe
evolution. However, our leading idea is to also keep track of the mass at the
boundary\r\nby working with measures defined on the whole closure Ω . The driving
functional is a\r\nmodification of the classical relative entropy that also makes
use of the information at the\r\nboundary. As an intermediate result, when Ω is
an interval in R1, we find a formula for the\r\ndescending slope of this geodesically
nonconvex functional."
acknowledgement: The author would like to thank Jan Maas for suggesting this project
and for many helpful comments, Antonio Agresti, Lorenzo Dello Schiavo and Julian
Fischer for several fruitful discussions, Oliver Tse for pointing out the reference
[10], and the anonymous reviewer for carefully reading this manuscript and providing
valuable suggestions. He also gratefully acknowledges support from the Austrian
Science Fund (FWF) project 10.55776/F65.Open access funding provided by Institute
of Science and Technology (IST Austria).
article_number: '23'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Filippo
full_name: Quattrocchi, Filippo
id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308
last_name: Quattrocchi
orcid: 0009-0000-9773-1931
citation:
ama: Quattrocchi F. Variational structures for the Fokker-Planck equation with general
Dirichlet boundary conditions. Calculus of Variations and Partial Differential
Equations. 2026;65(1). doi:10.1007/s00526-025-03193-1
apa: Quattrocchi, F. (2026). Variational structures for the Fokker-Planck equation
with general Dirichlet boundary conditions. Calculus of Variations and Partial
Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-025-03193-1
chicago: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation
with General Dirichlet Boundary Conditions.” Calculus of Variations and Partial
Differential Equations. Springer Nature, 2026. https://doi.org/10.1007/s00526-025-03193-1.
ieee: F. Quattrocchi, “Variational structures for the Fokker-Planck equation with
general Dirichlet boundary conditions,” Calculus of Variations and Partial
Differential Equations, vol. 65, no. 1. Springer Nature, 2026.
ista: Quattrocchi F. 2026. Variational structures for the Fokker-Planck equation
with general Dirichlet boundary conditions. Calculus of Variations and Partial
Differential Equations. 65(1), 23.
mla: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation
with General Dirichlet Boundary Conditions.” Calculus of Variations and Partial
Differential Equations, vol. 65, no. 1, 23, Springer Nature, 2026, doi:10.1007/s00526-025-03193-1.
short: F. Quattrocchi, Calculus of Variations and Partial Differential Equations
65 (2026).
corr_author: '1'
date_created: 2025-12-29T12:06:26Z
date_published: 2026-01-01T00:00:00Z
date_updated: 2026-04-07T08:37:46Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-025-03193-1
external_id:
arxiv:
- '2403.07803'
file:
- access_level: open_access
checksum: 635370d64abaf444f50f5cca60bba1be
content_type: application/pdf
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date_created: 2026-01-05T12:36:39Z
date_updated: 2026-01-05T12:36:39Z
file_id: '20945'
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file_date_updated: 2026-01-05T12:36:39Z
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language:
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month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Variational structures for the Fokker-Planck equation with general Dirichlet
boundary conditions
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 65
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '21658'
abstract:
- lang: eng
text: Dipolar (ℓ = 1) mixed modes have revealed a surprisingly weak differential
rotation between the core and the envelope of evolved solar-like stars. Quadrupolar
(ℓ = 2) mixed modes also contain information regarding internal dynamics but are
very rarely characterised due to their low amplitude and the challenging identification
of adjacent or overlapping rotationally split multiplets affected by near-degeneracy
effects. We aim to extend the broadly used asymptotic seismic diagnostics beyond
ℓ = 1 mixed modes by developing an analogue asymptotic description of ℓ = 2 mixed
modes while explicitly accounting for near-degeneracy effects that distort their
rotational multiplets. We have derived a new asymptotic formulation of near-degenerate
mixed ℓ = 2 modes that describes off-diagonal terms representing the interaction
between modes of adjacent radial orders. This formalism, expressed directly in
the mixed-mode basis, provides analytical expressions for the near-degeneracy
effects. We implemented the formalism within a global Bayesian mode-fitting framework
for a direct fit of all ℓ = 0, 1, 2 modes in the power spectrum density. We were
able to asymptotically model the asymmetric rotational splitting present in various
radial orders of ℓ = 2 modes observed in young red giant stars without the need
for any numerical stellar modelling. We applied our formalism to the Kepler target
KIC 7341231, and it yielded core and envelope rotation rates consistent with previous
numerical modelling while providing improved constraints from the global and model-independent
approach. We also characterised the new target, KIC 8179973, measuring its rotation
rate and mixed-mode parameters for the first time. As our framework relies on
a direct global fit, it allows for much better precision on the asteroseismic
parameters and rotation rate estimates than standard methods, yielding better
constraints for rotation inversions. We have placed the first observational constraints
on the asymptotic ℓ = 2 mixed-mode parameters (ΔΠ2, q2, and εg, 2), thus paving
the way towards the use of asymptotic seismology beyond ℓ = 1 mixed modes.
acknowledgement: 'We thank the referee for their careful and constructive report,
which has substantially enhanced both the quality and clarity of the manuscript.
L. Bugnet and L. Einramhof gratefully acknowledge support from the European Research
Council (ERC) under the Horizon Europe programme (Calcifer; Starting Grant agreement
N°101165631). 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. The authors acknowledge
the great support and feedback provided during the redaction of this article by
Pr. Rafael García and Pr. Savita Mathur. We would also like to thank Dr. Emily Hatt
for her insights on uncertainty estimates. The authors also thank the members of
the Asteroseismology and Stellar Dynamics group of the Institute of Science and
Technology Austria (ISTA) for very useful discussions: L. Barrault, S.B. Das, K.
Smith. This paper includes data collected by the Kepler mission and obtained from
the MAST data archive at the Space Telescope Science Institute (STScI). Funding
for the Kepler mission is provided by the NASA Science Mission Directorate. STScI
is operated by the Association of Universities for Research in Astronomy, Inc.,
under NASA contract NAS 5–26555. Software: AstroPy (Astropy Collaboration 2013,
2018), Matplotlib (Hunter 2007), NumPy (Harris et al. 2020), SciPy (Virtanen et
al. 2020), emcee (Foreman-Mackey et al. 2013), celerite (Foreman-Mackey et al. 2017),
slepc4py (Dalcin et al. 2011; Hernandez et al. 2005), KADACS (García et al. 2011),
sloscillations (Kuszlewicz et al. 2019, 2023).'
article_number: A321
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bastien Raymond Bernard
full_name: Liagre, Bastien Raymond Bernard
id: 662f1873-cab4-11f0-a719-8087d302868d
last_name: Liagre
- first_name: Aayush A
full_name: Desai, Aayush A
id: 502cfd30-32c1-11ee-a9a4-d8dad5c6739e
last_name: Desai
- first_name: Lukas
full_name: Einramhof, Lukas
id: f1497a1a-72ef-11ef-b75a-fd877bbf6e8c
last_name: Einramhof
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: 'Liagre BRB, Desai AA, Einramhof L, Bugnet LA. Near-degeneracy effects in quadrupolar
mixed modes: From an asymptotic description to data fitting. Astronomy and
Astrophysics. 2026;707. doi:10.1051/0004-6361/202558023'
apa: 'Liagre, B. R. B., Desai, A. A., Einramhof, L., & Bugnet, L. A. (2026).
Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description
to data fitting. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202558023'
chicago: 'Liagre, Bastien Raymond Bernard, Aayush A Desai, Lukas Einramhof, and
Lisa Annabelle Bugnet. “Near-Degeneracy Effects in Quadrupolar Mixed Modes: From
an Asymptotic Description to Data Fitting.” Astronomy and Astrophysics.
EDP Sciences, 2026. https://doi.org/10.1051/0004-6361/202558023.'
ieee: 'B. R. B. Liagre, A. A. Desai, L. Einramhof, and L. A. Bugnet, “Near-degeneracy
effects in quadrupolar mixed modes: From an asymptotic description to data fitting,”
Astronomy and Astrophysics, vol. 707. EDP Sciences, 2026.'
ista: 'Liagre BRB, Desai AA, Einramhof L, Bugnet LA. 2026. Near-degeneracy effects
in quadrupolar mixed modes: From an asymptotic description to data fitting. Astronomy
and Astrophysics. 707, A321.'
mla: 'Liagre, Bastien Raymond Bernard, et al. “Near-Degeneracy Effects in Quadrupolar
Mixed Modes: From an Asymptotic Description to Data Fitting.” Astronomy and
Astrophysics, vol. 707, A321, EDP Sciences, 2026, doi:10.1051/0004-6361/202558023.'
short: B.R.B. Liagre, A.A. Desai, L. Einramhof, L.A. Bugnet, Astronomy and Astrophysics
707 (2026).
corr_author: '1'
date_created: 2026-04-05T22:01:32Z
date_published: 2026-03-01T00:00:00Z
date_updated: 2026-04-07T09:01:44Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
- _id: IlCa
- _id: GradSch
doi: 10.1051/0004-6361/202558023
external_id:
arxiv:
- '2511.05314 '
file:
- access_level: open_access
checksum: 560cac19dc70184626b85e71a26ee22e
content_type: application/pdf
creator: dernst
date_created: 2026-04-07T09:00:50Z
date_updated: 2026-04-07T09:00:50Z
file_id: '21664'
file_name: 2026_AstronomyAstrophysics_Liagre.pdf
file_size: 12287607
relation: main_file
success: 1
file_date_updated: 2026-04-07T09:00:50Z
has_accepted_license: '1'
intvolume: ' 707'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description
to data fitting'
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: 707
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21657'
abstract:
- lang: eng
text: We compare three global kilometer-scale models (ICON, IFS and NICAM) to clarify
the advantages and challenges of high-resolution global weather and climate modeling,
using different approaches to represent convection, from fully parameterized to
fully explicit. Our analysis focuses on tropical precipitation characteristics
spanning a wide range of spatio-temporal scales—including the diurnal cycle, extreme
precipitation, convective organization, and the Madden-Julian Oscillation (MJO)—along
with interactions between convection and the thermodynamic environment. All three
models commonly show weaker convective organization with smaller precipitation
cells than observed, though the strength of the bias varies by model. This diversity
is introduced by differences in the representation of (a) convective initiation
affected by the convective sensitivity to moisture and (b) tropospheric moistening
associated with deep convection. Models with stronger thermodynamic-convection
coupling increase environmental moisture near convection, thereby enhancing convective
organization. This has important upscale effects on the MJO; while IFS and NICAM
capture its eastward propagation well, ICON has difficulty reproducing it. The
amplitudes and phases of precipitation diurnal cycles over land show much greater
disagreement among the models than over ocean, influenced by how convection is
initiated. Biases in rain evaporation and cold pool formation hinder the propagation
of mesoscale convection, leading to errors such as the misrepresentation of nocturnal
convection moving off the coast of Sumatra in IFS and ICON. These results highlight
the importance of thermodynamic-convection coupling in realistically simulating
tropical convection across scales. To improve this coupling, kilometer-scale models
require better representation of the interaction between resolved convection and
three-dimensional turbulent mixing.
acknowledgement: 'We thank Peter Bechtold, Lukas Brunner, Peter Dueben, Richard Forbes,
Estibaliz Gascon, and Benoit Vanniere for providing insightful comments on the present
study. We also thank Sebastian Milinski, Xabier Pedruzo and Thomas Rackow for their
contributions to setting up IFS-FESOM for nextGEMS. We are also grateful to Dr.
Walter Hannah and an anonymous reviewer for their constructive comments, which improved
the original version of the manuscript. D. Takasuka was supported by JSPS KAKENHI
Grants 20H05728 and 24K22893 and by JSPS Core-to-Core Program, “International Core-to-Core
Project on Global Storm Resolving Analysis” (Grant Number: JPJSCCA20220001). T.
Becker was supported by the Horizon 2020 project nextGEMS under grant agreement
number 101003470. J. Bao acknowledges funding from the European Union''s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant
agreement No 101034413). The ICON and IFS simulations were performed with supercomputing
resources of the German Climate Computing Centre (Deutsches Klimarechenzentrum,
DKRZ) granted by its Scientific Steering Committee (WLA) under project ID 1235.
The NICAM simulation was performed on the supercomputer Fugaku (proposal numbers
hp220132, hp230078, hp230108, hp230278, and hp240267).'
article_number: e2025MS005343
article_processing_charge: Yes
article_type: original
author:
- first_name: Daisuke
full_name: Takasuka, Daisuke
last_name: Takasuka
- first_name: Tobias
full_name: Becker, Tobias
last_name: Becker
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
citation:
ama: Takasuka D, Becker T, Bao J. Precipitation characteristics and thermodynamic-convection
coupling in global kilometer-scale simulations. Journal of Advances in Modeling
Earth Systems. 2026;18(3). doi:10.1029/2025MS005343
apa: Takasuka, D., Becker, T., & Bao, J. (2026). Precipitation characteristics
and thermodynamic-convection coupling in global kilometer-scale simulations. Journal
of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2025MS005343
chicago: Takasuka, Daisuke, Tobias Becker, and Jiawei Bao. “Precipitation Characteristics
and Thermodynamic-Convection Coupling in Global Kilometer-Scale Simulations.”
Journal of Advances in Modeling Earth Systems. Wiley, 2026. https://doi.org/10.1029/2025MS005343.
ieee: D. Takasuka, T. Becker, and J. Bao, “Precipitation characteristics and thermodynamic-convection
coupling in global kilometer-scale simulations,” Journal of Advances in Modeling
Earth Systems, vol. 18, no. 3. Wiley, 2026.
ista: Takasuka D, Becker T, Bao J. 2026. Precipitation characteristics and thermodynamic-convection
coupling in global kilometer-scale simulations. Journal of Advances in Modeling
Earth Systems. 18(3), e2025MS005343.
mla: Takasuka, Daisuke, et al. “Precipitation Characteristics and Thermodynamic-Convection
Coupling in Global Kilometer-Scale Simulations.” Journal of Advances in Modeling
Earth Systems, vol. 18, no. 3, e2025MS005343, Wiley, 2026, doi:10.1029/2025MS005343.
short: D. Takasuka, T. Becker, J. Bao, Journal of Advances in Modeling Earth Systems
18 (2026).
corr_author: '1'
date_created: 2026-04-05T22:01:31Z
date_published: 2026-03-01T00:00:00Z
date_updated: 2026-04-07T09:14:51Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2025MS005343
ec_funded: 1
file:
- access_level: open_access
checksum: ca7dac4bab31348d0640ed22580c6dce
content_type: application/pdf
creator: dernst
date_created: 2026-04-07T09:11:23Z
date_updated: 2026-04-07T09:11:23Z
file_id: '21665'
file_name: 2026_JAMES_Takasuka.pdf
file_size: 3854313
relation: main_file
success: 1
file_date_updated: 2026-04-07T09:11:23Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: None
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Precipitation characteristics and thermodynamic-convection coupling in global
kilometer-scale simulations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '21659'
abstract:
- lang: eng
text: The recent detection of solar equatorial Rossby waves has renewed interest
in the study of gravito-inertial waves propagating in the convective envelope
of solar-type stars. In particular, the ability of these envelope gravito-inertial
modes to couple with those trapped in the radiative interior could open up new
opportunities for probing the deep-layer dynamics of solar-type stars. The possibility
for such a coupling to occur is particularly favoured among pre-main-sequence
(PMS) solar-type stars. Indeed, due to the contraction of the protostellar object,
they are able to reach high rotation frequencies before nuclear reactions are
ignited and magnetic braking becomes the driving mechanism for their rotational
evolution. In this work, we studied the coupling between the envelope inertial
waves and the radiative interior g modes in PMS stars, focussing on the case of
prograde dipolar modes. We considered the cases of 0.5 M⊙ and 1 M⊙ PMS models,
each with three different scenarios of rotational evolution. We show that for
stars that have formed with a sufficient amount of angular momentum, this coupling
can occur in frequency ranges that are accessible to space-borne photometry, creating
inertial dips in the period spacing pattern. Using an asymptotic analysis, we
characterised the shape of these inertial dips to show that they depend on rotation
and on the stiffness of the convective-radiative interface.
acknowledgement: 'The authors want to thank the anonymous referee for useful comments.
SNB acknowledges support from PLATO ASI-INAF agreement no. 2022-28-HH.0 “PLATO Fase
D”. SNB and AFL acknowledge support from the INAF grant MASTODINT. CP thanks the
Belgian Federal Science Policy Office (BELSPO) for the financial support in the
framework of the PRODEX Program of the European Space Agency (ESA) under contract
number 4000141194. S.M acknowledges support from the CNES GOLF-SOHO and PLATO grants
at CEA/DAp. LB and SM gratefully acknowledge support from the European Research
Council (ERC) under the Horizon Europe programme (LB: Calcifer; Starting Grant agreement
N°101165631; SM: 4D-STAR; Synergy Grant agreement N°101071505). 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. The authors acknowledge G. Buldgen, H. Dhouib,
and M.A. Dupret for fruitful discussions.'
article_number: L16
article_processing_charge: No
article_type: letter_editor
arxiv: 1
author:
- first_name: S. N.
full_name: Breton, S. N.
last_name: Breton
- first_name: C.
full_name: Pezzotti, C.
last_name: Pezzotti
- first_name: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: M. P.
full_name: Di Mauro, M. P.
last_name: Di Mauro
- first_name: J.
full_name: Joergensen, J.
last_name: Joergensen
- first_name: K.
full_name: Zwintz, K.
last_name: Zwintz
- first_name: A. F.
full_name: Lanza, A. F.
last_name: Lanza
citation:
ama: Breton SN, Pezzotti C, Mathis S, et al. Core-envelope coupling of gravito-inertial
waves in pre-main-sequence solar-type stars. Astronomy & Astrophysics.
2026;707. doi:10.1051/0004-6361/202659309
apa: Breton, S. N., Pezzotti, C., Mathis, S., Bugnet, L. A., Di Mauro, M. P., Joergensen,
J., … Lanza, A. F. (2026). Core-envelope coupling of gravito-inertial waves in
pre-main-sequence solar-type stars. Astronomy & Astrophysics. Wiley.
https://doi.org/10.1051/0004-6361/202659309
chicago: Breton, S. N., C. Pezzotti, S. Mathis, Lisa Annabelle Bugnet, M. P. Di
Mauro, J. Joergensen, K. Zwintz, and A. F. Lanza. “Core-Envelope Coupling of Gravito-Inertial
Waves in Pre-Main-Sequence Solar-Type Stars.” Astronomy & Astrophysics.
Wiley, 2026. https://doi.org/10.1051/0004-6361/202659309.
ieee: S. N. Breton et al., “Core-envelope coupling of gravito-inertial waves
in pre-main-sequence solar-type stars,” Astronomy & Astrophysics, vol.
707. Wiley, 2026.
ista: Breton SN, Pezzotti C, Mathis S, Bugnet LA, Di Mauro MP, Joergensen J, Zwintz
K, Lanza AF. 2026. Core-envelope coupling of gravito-inertial waves in pre-main-sequence
solar-type stars. Astronomy & Astrophysics. 707, L16.
mla: Breton, S. N., et al. “Core-Envelope Coupling of Gravito-Inertial Waves in
Pre-Main-Sequence Solar-Type Stars.” Astronomy & Astrophysics, vol.
707, L16, Wiley, 2026, doi:10.1051/0004-6361/202659309.
short: S.N. Breton, C. Pezzotti, S. Mathis, L.A. Bugnet, M.P. Di Mauro, J. Joergensen,
K. Zwintz, A.F. Lanza, Astronomy & Astrophysics 707 (2026).
date_created: 2026-04-05T22:01:32Z
date_published: 2026-03-01T00:00:00Z
date_updated: 2026-04-07T09:23:27Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202659309
external_id:
arxiv:
- '2603.01979'
file:
- access_level: open_access
checksum: a7fd798bf450d67d4166fdf54ff2c70c
content_type: application/pdf
creator: dernst
date_created: 2026-04-07T09:20:02Z
date_updated: 2026-04-07T09:20:02Z
file_id: '21666'
file_name: 2026_AstronomyAstrophysics_Breton.pdf
file_size: 1535506
relation: main_file
success: 1
file_date_updated: 2026-04-07T09:20:02Z
has_accepted_license: '1'
intvolume: ' 707'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _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: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type
stars
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: 707
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21660'
abstract:
- lang: eng
text: Kapitza-Dirac scattering, the diffraction of matter waves from a standing
light field, is widely utilized in ultracold gases, but its behavior in the strongly
interacting regime is an open question. Here, we develop a numerically exact two-body
description of Kapitza-Dirac scattering for two contact-interacting atoms in a
one-dimensional harmonic trap subjected to a pulsed optical lattice, enabling
us to obtain the numerically exact dynamics. We map how interaction strength,
lattice depth, lattice wave number, and pulse duration reshape the diffraction
pattern, leading to an interaction-dependent population redistribution in real
and momentum space. By comparing the exact dynamics to an impulsive sudden-approximation
description, we delineate the parameter regimes where it remains accurate and
those, notably at strong attraction and small lattice wave number, where it fails.
Our results provide a controlled few-body benchmark for interacting Kapitza-Dirac
scattering and quantitative guidance for Kapitza-Dirac-based probes of ultracold
atomic systems.
acknowledgement: We thank Max Hachmann, Andreas Hemmerich, and Yann Kiefer for valuable
discussions. This work has been funded by the Cluster of Excellence “Advanced Imaging
of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID
390715994. G.M.K. has received funding by the Austrian Science Fund (FWF) 10.55776/F1004.
article_number: '013297'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Becker, A.
last_name: Becker
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Becker A, Koutentakis G, Schmelcher P. Two-body Kapitza-Dirac scattering of
one-dimensional ultracold atoms. Physical Review Research. 2026;8. doi:10.1103/rdsn-stlq
apa: Becker, A., Koutentakis, G., & Schmelcher, P. (2026). Two-body Kapitza-Dirac
scattering of one-dimensional ultracold atoms. Physical Review Research.
American Physical Society. https://doi.org/10.1103/rdsn-stlq
chicago: Becker, A., Georgios Koutentakis, and P. Schmelcher. “Two-Body Kapitza-Dirac
Scattering of One-Dimensional Ultracold Atoms.” Physical Review Research.
American Physical Society, 2026. https://doi.org/10.1103/rdsn-stlq.
ieee: A. Becker, G. Koutentakis, and P. Schmelcher, “Two-body Kapitza-Dirac scattering
of one-dimensional ultracold atoms,” Physical Review Research, vol. 8.
American Physical Society, 2026.
ista: Becker A, Koutentakis G, Schmelcher P. 2026. Two-body Kapitza-Dirac scattering
of one-dimensional ultracold atoms. Physical Review Research. 8, 013297.
mla: Becker, A., et al. “Two-Body Kapitza-Dirac Scattering of One-Dimensional Ultracold
Atoms.” Physical Review Research, vol. 8, 013297, American Physical Society,
2026, doi:10.1103/rdsn-stlq.
short: A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 8 (2026).
corr_author: '1'
date_created: 2026-04-05T22:01:32Z
date_published: 2026-03-18T00:00:00Z
date_updated: 2026-04-07T09:37:57Z
day: '18'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/rdsn-stlq
external_id:
arxiv:
- '2512.15260'
file:
- access_level: open_access
checksum: 339bff9d13486a8028049404988b9b0b
content_type: application/pdf
creator: dernst
date_created: 2026-04-07T09:34:31Z
date_updated: 2026-04-07T09:34:31Z
file_id: '21667'
file_name: 2026_PhysicalReviewResearch_Becker.pdf
file_size: 2131627
relation: main_file
success: 1
file_date_updated: 2026-04-07T09:34:31Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3
grant_number: F100403
name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '21661'
abstract:
- lang: eng
text: Model checking undiscounted reachability and expected-reward properties on
Markov decision processes (MDPs) are key for the verification of systems that
act under uncertainty. Popular algorithms are policy iteration and variants of
value iteration; in tool competitions, most participants rely on the latter. These
algorithms generally need worst-case exponential time. However, the problem can
equally be formulated as a linear programme, solvable in polynomial time. In this
paper, we give a detailed overview of today’s state-of-the-art algorithms for
MDP model checking with a focus on performance and correctness. We highlight their
fundamental differences, and describe various optimizations and implementation
variants. We experimentally compare floating-point and exact-arithmetic implementations
of all algorithms on three benchmark sets using two probabilistic model checkers.
Our results show that (optimistic) value iteration is a sensible default, but
other algorithms are preferable in specific settings. This paper thereby provides
a guide for MDP verification practitioners—tool builders and users alike.
acknowledgement: "This research was funded by the European Union’s Horizon 2020 research
and innovation programme under Marie Skłodowska-Curie grant agreements 101008233
(MISSION)\r\nand 101034413 (IST-BRIDGE), by the Interreg North Sea project STORM_SAFE,
by a KI-Starter grant from the Ministerium für Kultur und Wissenschaft NRW, by NWO
VENI grant no. 639.021.754, and by NWO VIDI grant VI.Vidi.223.110 (TruSTy). Experiments
were performed with computing resources granted by RWTH Aachen University under
project rwth1632."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Arnd
full_name: Hartmanns, Arnd
last_name: Hartmanns
- first_name: Sebastian
full_name: Junges, Sebastian
last_name: Junges
- first_name: Tim
full_name: Quatmann, Tim
last_name: Quatmann
- first_name: Maximilian
full_name: Weininger, Maximilian
id: 02ab0197-cc70-11ed-ab61-918e71f56881
last_name: Weininger
orcid: 0000-0002-0163-2152
citation:
ama: Hartmanns A, Junges S, Quatmann T, Weininger M. The revised practitioner’s
guide to MDP model checking algorithms. International Journal on Software Tools
for Technology Transfer. 2026. doi:10.1007/s10009-026-00848-y
apa: Hartmanns, A., Junges, S., Quatmann, T., & Weininger, M. (2026). The revised
practitioner’s guide to MDP model checking algorithms. International Journal
on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-026-00848-y
chicago: Hartmanns, Arnd, Sebastian Junges, Tim Quatmann, and Maximilian Weininger.
“The Revised Practitioner’s Guide to MDP Model Checking Algorithms.” International
Journal on Software Tools for Technology Transfer. Springer Nature, 2026.
https://doi.org/10.1007/s10009-026-00848-y.
ieee: A. Hartmanns, S. Junges, T. Quatmann, and M. Weininger, “The revised practitioner’s
guide to MDP model checking algorithms,” International Journal on Software
Tools for Technology Transfer. Springer Nature, 2026.
ista: Hartmanns A, Junges S, Quatmann T, Weininger M. 2026. The revised practitioner’s
guide to MDP model checking algorithms. International Journal on Software Tools
for Technology Transfer.
mla: Hartmanns, Arnd, et al. “The Revised Practitioner’s Guide to MDP Model Checking
Algorithms.” International Journal on Software Tools for Technology Transfer,
Springer Nature, 2026, doi:10.1007/s10009-026-00848-y.
short: A. Hartmanns, S. Junges, T. Quatmann, M. Weininger, International Journal
on Software Tools for Technology Transfer (2026).
date_created: 2026-04-05T22:01:32Z
date_published: 2026-03-09T00:00:00Z
date_updated: 2026-04-07T09:52:54Z
day: '09'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s10009-026-00848-y
ec_funded: 1
has_accepted_license: '1'
keyword:
- Quantitative model checking
- Markov decision process
- Linear programming
- Value iteration
- Policy iteration
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10009-026-00848-y
month: '03'
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: International Journal on Software Tools for Technology Transfer
publication_identifier:
eissn:
- 1433-2787
issn:
- 1433-2779
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '21668'
relation: software
status: public
scopus_import: '1'
status: public
title: The revised practitioner’s guide to MDP model checking algorithms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...