---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20851'
abstract:
- lang: eng
text: High-voltage disordered spinel LiNi0.5Mn1.5O4 is a promising cathode material
for high power density in lithium-ion batteries. However, it suffers from poor
cycle life associated with the rock-salt phase transformation. This study presents
a straightforward synthesis approach to enhance the electrochemical performance
of LiNi0.5Mn1.5O4 through a synergistic solid-state modification with LiF and
AlF3. This dual modification promotes rapid Li⁺ diffusion, enables near-complete
delithiation/lithiation, approaching the theoretical capacity of disordered LiNi0.5Mn1.5O4,
and, more importantly, effectively mitigates the formation of the rock-salt phase,
thereby enhancing structural stability, as confirmed by operando X-ray absorption
spectroscopy (XAS) and synchrotron X-ray diffraction (SXRD). As a result, the
optimized LiNi0.5Mn1.5O4 (10 mg AlF3 + 30 mg LiF) delivers high reversible capacities
of 142.1, 139.1, 129.2, 121.6, 110.3, 93.5, and 76.1 mAh∙g−1 at 0.2C, 0.5C, 1.0C,
2.0C, 3.0C, 4.0C, and 5.0C, respectively. Full cells using graphite as the anode
and a high-loading cathode exhibit excellent cycling performance. They retain
80% of their capacity after 200 cycles at 0.5C within a voltage window of 3.5–4.9
V with cathode loading of 11 mg∙cm−2. The findings of this study will significantly
advance high-power LiNi0.5Mn1.5O4 materials, offering improved battery life and
thereby enhancing their potential for practical applications.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: 'This work was supported by the European Commission-financed project
IntelLigent (HORIZON-CL5-2021-D2-01-02) with project ID number 101069765. In collaboration
with ALBA staff, the operando SXRD and XAS experiments were performed at BL-16-NOTOS
beamline at ALBA Synchrotron Light Source (experiment number: 2023097765). This
research was supported by the Scientific Service Units (SSU) of the Institute of
Science and Technology Austria (ISTA) through resources provided by the Electron
Microscopy Facility (EMF) and the Nanofabrication Facility (NFF), and M.I. and S.H.
acknowledge financial support from ISTA and the Werner Siemens Foundation. Jordi
Jacas Biendicho acknowledges the fellowship RYC2021-034994-I, funded by MICIU/AEI/10.13039/501100011033
and the European Union «NextGenerationEU»/PRTR». Jordi Llorca is a Serra Húnter
Fellow and is grateful to projects MICIN/AEI/FEDER PID2021-124572OB-C31 and Maria
de Maeztu Units of Excellence Programme CEX2023-001300-M, and GC 2021 SGR 01061.'
article_number: e15962
article_processing_charge: Yes
article_type: original
author:
- first_name: Xingqi
full_name: Chang, Xingqi
last_name: Chang
- first_name: Carlos
full_name: Escudero, Carlos
last_name: Escudero
- first_name: Ashley P.
full_name: Black, Ashley P.
last_name: Black
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Elías
full_name: Martínez, Elías
last_name: Martínez
- first_name: Xuan
full_name: Lu, Xuan
last_name: Lu
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Jordi Jacas
full_name: Biendicho, Jordi Jacas
last_name: Biendicho
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Chang X, Escudero C, Black AP, et al. Mitigating the rock-salt phase transformation
in disordered LNMO through synergetic solid-state AlF3/LiF modifications. Advanced
Science. 2026;13(11). doi:10.1002/advs.202515962
apa: Chang, X., Escudero, C., Black, A. P., Horta, S., Martínez, E., Lu, X., … Cabot,
A. (2026). Mitigating the rock-salt phase transformation in disordered LNMO through
synergetic solid-state AlF3/LiF modifications. Advanced Science. Wiley.
https://doi.org/10.1002/advs.202515962
chicago: Chang, Xingqi, Carlos Escudero, Ashley P. Black, Sharona Horta, Elías Martínez,
Xuan Lu, Jordi Llorca, Maria Ibáñez, Jordi Jacas Biendicho, and Andreu Cabot.
“Mitigating the Rock-Salt Phase Transformation in Disordered LNMO through Synergetic
Solid-State AlF3/LiF Modifications.” Advanced Science. Wiley, 2026. https://doi.org/10.1002/advs.202515962.
ieee: X. Chang et al., “Mitigating the rock-salt phase transformation in
disordered LNMO through synergetic solid-state AlF3/LiF modifications,” Advanced
Science, vol. 13, no. 11. Wiley, 2026.
ista: Chang X, Escudero C, Black AP, Horta S, Martínez E, Lu X, Llorca J, Ibáñez
M, Biendicho JJ, Cabot A. 2026. Mitigating the rock-salt phase transformation
in disordered LNMO through synergetic solid-state AlF3/LiF modifications. Advanced
Science. 13(11), e15962.
mla: Chang, Xingqi, et al. “Mitigating the Rock-Salt Phase Transformation in Disordered
LNMO through Synergetic Solid-State AlF3/LiF Modifications.” Advanced Science,
vol. 13, no. 11, e15962, Wiley, 2026, doi:10.1002/advs.202515962.
short: X. Chang, C. Escudero, A.P. Black, S. Horta, E. Martínez, X. Lu, J. Llorca,
M. Ibáñez, J.J. Biendicho, A. Cabot, Advanced Science 13 (2026).
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
from the corresponding author upon reasonable request
date_created: 2025-12-21T23:01:35Z
date_published: 2026-02-23T00:00:00Z
date_updated: 2026-07-23T06:18:43Z
day: '23'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/advs.202515962
external_id:
pmid:
- '41388041'
file:
- access_level: open_access
checksum: 37adc3eff9ad9f8f9b55cfe66883f36d
content_type: application/pdf
creator: dernst
date_created: 2026-07-23T06:15:51Z
date_updated: 2026-07-23T06:15:51Z
file_id: '22387'
file_name: 2026_AdvancedScience_Chang.pdf
file_size: 6353217
relation: main_file
success: 1
file_date_updated: 2026-07-23T06:15:51Z
fulldoi: https://doi.org/10.1002/advs.202515962
has_accepted_license: '1'
intvolume: ' 13'
issue: '11'
keyword:
- disordered spinel LiNi0.5Mn1.5O4 (LNMO)
- generation 3b batteries
- operando SXRD
- operando XAS
- rock-salt
- solid-state synthesis
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Science
publication_identifier:
eissn:
- 2198-3844
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Mitigating the rock-salt phase transformation in disordered LNMO through synergetic
solid-state AlF3/LiF modifications
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: 13
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22956'
abstract:
- lang: eng
text: Tissue regeneration requires de novo patterning, which has been proposed to
be facilitated by cellular heterogeneity. Yet how such heterogeneities are integrated
with the mechanochemical state of the tissue and stabilized at the chromatin level
into stable, spatially organized fates remains poorly understood. Using in vivo
mouse intestinal regeneration models and organoids, we identify a critical density
regime that produces a permissive window for heterogeneity in the mechanosensor
Yes-associated protein 1 (YAP1). We show that YAP1 heterogeneity is coupled to
lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates
the permissive chromatin state to Delta-Notch supracellular feedback and lineage
commitment. This circuit generates fate bistability and preserves a memory of
transient YAP1 activity, thereby maintaining spatial patterning as tissues return
to homeostasis after injury. Together, our findings establish a multiscale framework
in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated
bistability, convert transient heterogeneity into stable and self-organized tissue
architecture.
acknowledgement: We thank the Liberali group, M. Verbeek, and C. Soneson for fruitful
discussions; E. Tagliavini for IT support; J. Lüthi for Fractal support; H. Köhler
for FACS sorting; T.O. Buchholz for help on cell segmentation; B. Treutlein and
A. Xavier da Silveira dos Santos for help with library preparation of single-cell
ATAC-seq; M. Garioni for help with mouse salivary organoids; M. Kahnwald for help
with human intestinal organoids; M. Lütolf, M. Nikolaev, and O. Mitrofanova for
providing material and initial training for microwell experiments; J. Tchorz and
V. Orsini for intestinal tissue sections of the YAP1 activator experiment in homeostasis;
R. Kageyama for DLL1-Venus-T2A-mCherry mice; J.-F. Spetz for technical assistance;
C. Lambert and N. Accart for help with sample preparation; Claudia Flandoli for
graphic design of schemes; and Zuzana Nascakova for the graphical abstract. We thank
the Foundation Hubrecht Organoid Technology (now Foundation Hubrecht Organoid Biobank,
https://www.hubrechtorganoidbiobank.org/) for the duodenal organoid line used in
this study (HUB-04-A2-001). We thank C.P. Heisenberg, M. Lütolf, C. Tsiairis, J.
Zaugg, G. D’Angelo, L. Giorgetti, S. Arber, and the Liberali group for reading the
manuscript. C.S. was supported by the European Molecular Biology Organization (Postdoctoral
Fellowship ALTF 660-2020) and the Human Frontier Science Program (HFSP) LT000746/2021-L.
D.B.B. was supported by the NOMIS Foundation as a NOMIS fellow, an EMBO Postdoctoral
Fellowship (ALTF 343-2022), and the Austrian Academy of Sciences through an APART-MINT
Fellowship. B.S. was supported by the Francis Crick Institute, which receives its
core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome
Trust (FC001159). This work received funding from ERC to E.H. (grant number 851288)
and to P.L. (grant number 758617) and from SNSF (310030_208162 and SNSF ERC TMCG-3_223263).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Silvia
full_name: Barbiero, Silvia
last_name: Barbiero
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Koen C.
full_name: Oost, Koen C.
last_name: Oost
- first_name: Clara
full_name: Baader, Clara
last_name: Baader
- first_name: Nicole A.
full_name: Repina, Nicole A.
last_name: Repina
- first_name: Jinse
full_name: Kim, Jinse
last_name: Kim
- first_name: Oscar E.
full_name: Diaz, Oscar E.
last_name: Diaz
- first_name: Isa
full_name: Uccelli, Isa
last_name: Uccelli
- first_name: Laura
full_name: Capolupo, Laura
last_name: Capolupo
- first_name: Ludivine Challet
full_name: Meylan, Ludivine Challet
last_name: Meylan
- first_name: Veronique
full_name: Kalck, Veronique
last_name: Kalck
- first_name: Franziska
full_name: Moos, Franziska
last_name: Moos
- first_name: Simon
full_name: Suppinger, Simon
last_name: Suppinger
- first_name: Qiutan
full_name: Yang, Qiutan
last_name: Yang
- first_name: Jakob
full_name: Schnabl, Jakob
last_name: Schnabl
- first_name: Umut
full_name: Kilik, Umut
last_name: Kilik
- first_name: Matthieu
full_name: Bourdon, Matthieu
last_name: Bourdon
- first_name: J. Gray
full_name: Camp, J. Gray
last_name: Camp
- first_name: Brigitta
full_name: Stockinger, Brigitta
last_name: Stockinger
- first_name: Alessandra
full_name: Ferrari, Alessandra
last_name: Ferrari
- first_name: Marc
full_name: Bühler, Marc
last_name: Bühler
- first_name: Michael B.
full_name: Stadler, Michael B.
last_name: Stadler
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
citation:
ama: Schwayer C, Barbiero S, Brückner D, et al. Multiscale integration of tissue
and chromatin context converts cell heterogeneity into stable intestinal patterning.
Cell. 2026;189(17):5266-5282.e17. doi:10.1016/j.cell.2026.06.009
apa: Schwayer, C., Barbiero, S., Brückner, D., Oost, K. C., Baader, C., Repina,
N. A., … Liberali, P. (2026). Multiscale integration of tissue and chromatin context
converts cell heterogeneity into stable intestinal patterning. Cell. Cell
Press. https://doi.org/10.1016/j.cell.2026.06.009
chicago: Schwayer, Cornelia, Silvia Barbiero, David Brückner, Koen C. Oost, Clara
Baader, Nicole A. Repina, Jinse Kim, et al. “Multiscale Integration of Tissue
and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.”
Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.06.009.
ieee: C. Schwayer et al., “Multiscale integration of tissue and chromatin
context converts cell heterogeneity into stable intestinal patterning,” Cell,
vol. 189, no. 17. Cell Press, p. 5266–5282.e17, 2026.
ista: Schwayer C, Barbiero S, Brückner D, Oost KC, Baader C, Repina NA, Kim J, Diaz
OE, Uccelli I, Capolupo L, Meylan LC, Kalck V, Moos F, Suppinger S, Yang Q, Schnabl
J, Kilik U, Bourdon M, Camp JG, Stockinger B, Ferrari A, Bühler M, Stadler MB,
Hannezo EB, Liberali P. 2026. Multiscale integration of tissue and chromatin context
converts cell heterogeneity into stable intestinal patterning. Cell. 189(17),
5266–5282.e17.
mla: Schwayer, Cornelia, et al. “Multiscale Integration of Tissue and Chromatin
Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” Cell,
vol. 189, no. 17, Cell Press, 2026, p. 5266–5282.e17, doi:10.1016/j.cell.2026.06.009.
short: C. Schwayer, S. Barbiero, D. Brückner, K.C. Oost, C. Baader, N.A. Repina,
J. Kim, O.E. Diaz, I. Uccelli, L. Capolupo, L.C. Meylan, V. Kalck, F. Moos, S.
Suppinger, Q. Yang, J. Schnabl, U. Kilik, M. Bourdon, J.G. Camp, B. Stockinger,
A. Ferrari, M. Bühler, M.B. Stadler, E.B. Hannezo, P. Liberali, Cell 189 (2026)
5266–5282.e17.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "All sequencing data have been deposited at the Gene Expression
Omnibus (GEO) under accession number GEO: GSE283662.\r\nAnalysis of imaging and
sequencing data was developed in the Liberali lab and is available at https://github.com/LiberaliLab/symmetry-breaking-2026.
Detailed information on the packages used is provided in the STAR Methods section.\r\nAny
additional information required to reanalyze the data reported in this paper is
available from the lead contact upon request."
date_created: 2026-09-17T11:06:12Z
date_published: 2026-08-20T00:00:00Z
date_updated: 2026-10-01T08:42:00Z
day: '20'
ddc:
- '570'
doi: 10.1016/j.cell.2026.06.009
ec_funded: 1
external_id:
pmid:
- '42379166'
file:
- access_level: open_access
checksum: 3ff0f4f8be0e79940ba11b18af318ae3
content_type: application/pdf
creator: dernst
date_created: 2026-10-01T08:34:11Z
date_updated: 2026-10-01T08:34:11Z
file_id: '23014'
file_name: 2026_Cell_Schwayer.pdf
file_size: 15536364
relation: main_file
success: 1
file_date_updated: 2026-10-01T08:34:11Z
fulldoi: https://doi.org/10.1016/j.cell.2026.06.009
has_accepted_license: '1'
intvolume: ' 189'
issue: '17'
keyword:
- tissue patterning
- heterogeneity
- mechanics
- intestinal regeneration
- epigenetic competence
- multiscale integration
- modeling
- organoids
- image-based phenotyping
- Yap1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 5266-5282.e17
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Multiscale integration of tissue and chromatin context converts cell heterogeneity
into stable intestinal patterning
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22974'
abstract:
- lang: eng
text: Far from being static structures, it is now well accepted that proteins are
highly dynamic entities even in the solid state. Here, we review recent progress
in application of magic-angle spinning (MAS) NMR for studying the site-specific
dynamics of proteins, as assessed using spin-relaxation and measurement of anisotropic
spin interactions. We focus on the types of experimental data that are available,
and how best to access the information which is provided by these experimental
measurements; in particular, we provide a retrospective on the field in light
of recent advances in analytical methodologies, which have led to a slow paradigm
shift in how we interpret relaxation rate constant measurements made in the solid
state.
acknowledgement: We thank the Austrian Science Fund (FWF, project number 10.55776/I5812)
for support. We are grateful to Petra Rovó (ISTA) for many insightful discussions.
article_number: '101615'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Benjamin
full_name: Tatman, Benjamin
id: 71cda2f3-e604-11ee-a1df-da10587eda3f
last_name: Tatman
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Tatman B, Schanda P. Quantifying fast protein dynamics by magic-angle spinning
NMR: Progress in experimental and analytical approaches. Progress in Nuclear
Magnetic Resonance Spectroscopy. 2026;156-157. doi:10.1016/j.pnmrs.2026.101615'
apa: 'Tatman, B., & Schanda, P. (2026). Quantifying fast protein dynamics by
magic-angle spinning NMR: Progress in experimental and analytical approaches.
Progress in Nuclear Magnetic Resonance Spectroscopy. Elsevier. https://doi.org/10.1016/j.pnmrs.2026.101615'
chicago: 'Tatman, Benjamin, and Paul Schanda. “Quantifying Fast Protein Dynamics
by Magic-Angle Spinning NMR: Progress in Experimental and Analytical Approaches.”
Progress in Nuclear Magnetic Resonance Spectroscopy. Elsevier, 2026. https://doi.org/10.1016/j.pnmrs.2026.101615.'
ieee: 'B. Tatman and P. Schanda, “Quantifying fast protein dynamics by magic-angle
spinning NMR: Progress in experimental and analytical approaches,” Progress
in Nuclear Magnetic Resonance Spectroscopy, vol. 156–157. Elsevier, 2026.'
ista: 'Tatman B, Schanda P. 2026. Quantifying fast protein dynamics by magic-angle
spinning NMR: Progress in experimental and analytical approaches. Progress in
Nuclear Magnetic Resonance Spectroscopy. 156–157, 101615.'
mla: 'Tatman, Benjamin, and Paul Schanda. “Quantifying Fast Protein Dynamics by
Magic-Angle Spinning NMR: Progress in Experimental and Analytical Approaches.”
Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 156–157, 101615,
Elsevier, 2026, doi:10.1016/j.pnmrs.2026.101615.'
short: B. Tatman, P. Schanda, Progress in Nuclear Magnetic Resonance Spectroscopy
156–157 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: No data was used for the research described in the article.
date_created: 2026-09-22T05:44:22Z
date_published: 2026-09-01T00:00:00Z
date_updated: 2026-10-06T13:00:47Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1016/j.pnmrs.2026.101615
fulldoi: https://doi.org/10.1016/j.pnmrs.2026.101615
has_accepted_license: '1'
keyword:
- Solid-state NMR
- Protein dynamics
- Magic-angle spinning
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.pnmrs.2026.101615
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Progress in Nuclear Magnetic Resonance Spectroscopy
publication_identifier:
eissn:
- 1873-3301
issn:
- 0079-6565
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Quantifying fast protein dynamics by magic-angle spinning NMR: Progress in
experimental and analytical approaches'
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: 156-157
year: '2026'
...
---
OA_place: publisher
_id: '22258'
abstract:
- lang: eng
text: "Uncovering the genetic architecture of complex traits and pinpointing causal
molecular drivers require the ability to distinguish true signals from noise within
massive, high-dimensional omics datasets. To extract meaningful biological insights
from these datasets, such as identifying causal genetic variants and proteins,
scalable and accurate inference methods are essential. To this end, this thesis
develops novel Bayesian inference frameworks based on Vector Approximate Message
Passing and demonstrates their effectiveness in the modeling of disease onset
times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce
gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that
enables the joint modeling of quantitative complex traits across millions of genetic
variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample
polygenic risk prediction compared to state-of-the-art approaches. We model human
height using 17 million whole-genome sequence variants from the UK Biobank, incorporating
a vast number of rare variants and revealing novel associations. gVAMP achieves
a prediction accuracy of approximately 46% for human height, representing the
highest reported performance for this trait to date. \r\n\r\nSecond, we present
vampW, a Bayesian framework for survival analysis applied to proteomic data. By
effectively handling right-censoring and complex protein dependencies within the
UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations
across 24 disease outcomes, the majority of which are not among the top marginal
discoveries. We further adjust protein levels for exponential age effects, yielding
1,308 associations and highlighting the sensitivity of the analysis to the chosen
age-correction methodology. Finally, vampW improves upon the variable selection
capabilities of the commonly used (penalized) variants of the Cox proportional
hazards model and delivers state-of-the-art out-of-sample prediction of disease
onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting
the genetic architecture of complex traits and the proteomic drivers of disease
onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions
of onset times, this work advances the capabilities of personalized medicine and
clinical risk stratification."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported in part by the Swiss National Science Foundation
through the\r\nEccellenza Grant \"Improving estimation and prediction of common
complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council
through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and
Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques
et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Al
full_name: Depope, Al
id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830
last_name: Depope
citation:
ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing
for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258'
apa: 'Depope, A. (2026). From sparse selection to risk prediction: Approximate
message passing for proteomic survival models and large-scale genomics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22258'
chicago: 'Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of
Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22258.'
ieee: 'A. Depope, “From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics,” Institute of
Science and Technology Austria, 2026.'
ista: 'Depope A. 2026. From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics. Institute of Science
and Technology Austria.'
mla: 'Depope, Al. From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics. Institute
of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22258.'
short: 'A. Depope, From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science
and Technology Austria, 2026.'
corr_author: '1'
das_tickbox: '1'
date_created: 2026-07-10T13:27:20Z
date_published: 2026-07-11T00:00:00Z
date_updated: 2026-10-20T09:03:21Z
day: '11'
ddc:
- '576'
- '610'
- '006'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaRo
- _id: MaMo
doi: 10.15479/AT-ISTA-22258
doi_confirm: '1'
file:
- access_level: open_access
checksum: 9ab386790515628d957a194f30a7ccb4
content_type: application/pdf
creator: adepope
date_created: 2026-07-13T14:52:19Z
date_updated: 2026-07-13T14:52:19Z
file_id: '22316'
file_name: 2026_Depope_Al_Thesis.pdf
file_size: 25109878
relation: main_file
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checksum: 8ed8fb63f76a695d5b6fec35343f4b90
content_type: application/zip
creator: adepope
date_created: 2026-07-13T14:56:41Z
date_updated: 2026-07-13T14:56:41Z
file_id: '22317'
file_name: 2026_Depope_Al_Thesis.zip
file_size: 1203199939
relation: source_file
file_date_updated: 2026-07-13T14:56:41Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22258
has_accepted_license: '1'
keyword:
- Approximate Message Passing
- GWAS
- Genomics
- Proteomics
- Survival modeling
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '169'
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf
grant_number: '101161364'
name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits'
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21488'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
title: 'From sparse selection to risk prediction: Approximate message passing for
proteomic survival models and large-scale genomics'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22511'
abstract:
- lang: eng
text: Wildfires are increasing in frequency, intensity, and extent globally due
to climate change and they can alter forest composition, structure, and function.
The destruction and subsequent regrowth of young vegetation can modify the ecosystem
evapotranspiration and downstream water availability. However, the response of
forest recovery on hydrology is not well known with even the sign of evapotranspiration
and water yield changes following forest fires being uncertain across the globe.
Here, we quantify the effects of forest regrowth after catastrophic wildfires
on evapotranspiration and runoff in the world's tallest angiosperm forest (Eucalyptus
regnans) in Australia. We combine eddy covariance measurements including pre-
and post-fire periods, mechanistic ecohydrological modeling and then extend the
analysis spatially to multiple fires in eucalypt-dominated forests in south-eastern
Australia by utilizing remote sensing. We find a fast recovery of evapotranspiration
which reaches and exceeds pre-fire values within 2 years after the bushfire, a
result confirmed by eddy covariance data, remote sensing, and modeling. Such a
fast evapotranspiration recovery is likely generalizable to tall eucalypt forests
in south-eastern Australia as shown by remote sensing. Once climate variability
is discounted, ecohydrological modeling shows evapotranspiration rates from the
recovering forest which reach peak values of +20% evapotranspiration 3 years post-fire.
As a result, modeled runoff decreases substantially. Contrary to previous research,
we find that the increase in modeled evapotranspiration is largely caused by the
aerodynamic effects of a much shorter forest height leading to higher surface
temperature, higher humidity gradients and therefore increased transpiration.
However, increases in evapotranspiration as well as decreases in runoff caused
by the young forest are constrained by energy and water limitations. Our result
of an increase in evapotranspiration due to aerodynamic warming in a shorter forest
after wildfires could occur in many parts of the world experiencing forest disturbances.
article_number: e16995
article_processing_charge: No
article_type: original
author:
- first_name: Naika
full_name: Meili, Naika
last_name: Meili
- first_name: Jason
full_name: Beringer, Jason
last_name: Beringer
- first_name: Jiacheng
full_name: Zhao, Jiacheng
last_name: Zhao
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
ama: Meili N, Beringer J, Zhao J, Fatichi S. Aerodynamic effects cause higher forest
evapotranspiration and water yield reductions after wildfires in tall forests.
Global Change Biology. 2024;30(1). doi:10.1111/gcb.16995
apa: Meili, N., Beringer, J., Zhao, J., & Fatichi, S. (2024). Aerodynamic effects
cause higher forest evapotranspiration and water yield reductions after wildfires
in tall forests. Global Change Biology. Wiley. https://doi.org/10.1111/gcb.16995
chicago: Meili, Naika, Jason Beringer, Jiacheng Zhao, and Simone Fatichi. “Aerodynamic
Effects Cause Higher Forest Evapotranspiration and Water Yield Reductions after
Wildfires in Tall Forests.” Global Change Biology. Wiley, 2024. https://doi.org/10.1111/gcb.16995.
ieee: N. Meili, J. Beringer, J. Zhao, and S. Fatichi, “Aerodynamic effects cause
higher forest evapotranspiration and water yield reductions after wildfires in
tall forests,” Global Change Biology, vol. 30, no. 1. Wiley, 2024.
ista: Meili N, Beringer J, Zhao J, Fatichi S. 2024. Aerodynamic effects cause higher
forest evapotranspiration and water yield reductions after wildfires in tall forests.
Global Change Biology. 30(1), e16995.
mla: Meili, Naika, et al. “Aerodynamic Effects Cause Higher Forest Evapotranspiration
and Water Yield Reductions after Wildfires in Tall Forests.” Global Change
Biology, vol. 30, no. 1, e16995, Wiley, 2024, doi:10.1111/gcb.16995.
short: N. Meili, J. Beringer, J. Zhao, S. Fatichi, Global Change Biology 30 (2024).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2026-08-11T05:51:07Z
day: '01'
doi: 10.1111/gcb.16995
extern: '1'
external_id:
pmid:
- '37916642'
fulldoi: https://doi.org/10.1111/gcb.16995
intvolume: ' 30'
issue: '1'
keyword:
- Aerodynamic effects
- Bushfires Australia
- Ecohydrological modeling
- Eddy covariancemeasurements
- Eucalyptus regnans
- Forest evapotranspiration
- Forest recovery
- Mountain Ash
- TERN OzFlux
- Wildfires
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/gcb.16995
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Global Change Biology
publication_identifier:
eissn:
- 1365-2486
issn:
- 1354-1013
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aerodynamic effects cause higher forest evapotranspiration and water yield
reductions after wildfires in tall forests
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: 30
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17219'
abstract:
- lang: eng
text: 'We introduce a multi-material non-manifold mesh-based surface tracking algorithm
that converts self-intersections into topological changes. Our algorithm generalizes
prior work on manifold surface tracking with topological changes: it preserves
surface features like mesh-based methods, and it robustly handles topological
changes like level set methods. Our method also offers improved efficiency and
robustness over the state of the art. We demonstrate the effectiveness of the
approach on a range of examples, including complex soap film simulations with
thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting
of millions of triangles.'
acknowledgement: Peter Heiss-Synak helped conceive the project, helped formulate the
algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data
structure, algorithm robustness and benchmarks, helped write the paper, and provided
supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed
ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm
robustness and benchmarks, optimized the performance, produced all results, most
figures, and the supplementary video, helped write the text, and provided conceptual
solutions throughout the project. Malina Strugaru helped implement the mesh data
structure and designed re-meshing operations for non-manifold triangle meshes. Arian
Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped
write the paper. Huidong Yang developed early prototypes for isosurface extraction
and visualization. Chris Wojtan helped conceive the project, helped write the paper,
and provided supervision, prototype grid data structure code, and conceptual solutions
throughout the project. We thank the anonymous reviewers for their helpful comments,
the members of the Visual Computing Group at ISTA for their feedback, Christopher
Batty for discussions about LosTopos, and SideFX for the Houdini Education software
licenses. This research was funded in part by the European Union (ERC-2021-COG
101045083 CoDiNA).
article_number: '54'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: Irina-Malina
full_name: Strugaru, Irina-Malina
id: 2afc607f-f128-11eb-9611-8f2a0dfcf074
last_name: Strugaru
- first_name: Arian
full_name: Etemadihaghighi, Arian
id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f
last_name: Etemadihaghighi
- first_name: Huidong
full_name: Yang, Huidong
last_name: Yang
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material
mesh-based surface tracking with implicit topology changes. ACM Transactions
on Graphics. 2024;43(4). doi:10.1145/3658223
apa: Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan,
C. (2024). Multi-material mesh-based surface tracking with implicit topology changes.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223
chicago: Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong
Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit
Topology Changes.” ACM Transactions on Graphics. Association for Computing
Machinery, 2024. https://doi.org/10.1145/3658223.
ieee: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan,
“Multi-material mesh-based surface tracking with implicit topology changes,” ACM
Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery,
2024.
ista: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material
mesh-based surface tracking with implicit topology changes. ACM Transactions on
Graphics. 43(4), 54.
mla: Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit
Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association
for Computing Machinery, 2024, doi:10.1145/3658223.
short: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM
Transactions on Graphics 43 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-07-10T12:24:00Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T11:19:25Z
day: '01'
ddc:
- '004'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3658223
external_id:
isi:
- '001289270900021'
file:
- access_level: open_access
checksum: 1917067d4b52d7729019b03560004e43
content_type: application/pdf
creator: dernst
date_created: 2024-07-23T06:35:15Z
date_updated: 2024-07-23T06:35:15Z
file_id: '17317'
file_name: 2024_ACMToG_HeissSynak.pdf
file_size: 48763368
relation: main_file
success: 1
- access_level: open_access
checksum: a4f0e293184bfa034c0c585848806b17
content_type: video/mp4
creator: akalinov
date_created: 2024-07-10T12:23:44Z
date_updated: 2024-07-10T12:23:44Z
file_id: '17221'
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file_size: 48021463
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success: 1
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content_type: application/pdf
creator: akalinov
date_created: 2025-11-11T09:50:52Z
date_updated: 2025-11-11T09:50:52Z
file_id: '20633'
file_name: SuperDuperTopoFixer.pdf
file_size: 48639581
relation: preprint
title: Authors' version of the text
file_date_updated: 2025-11-11T09:50:52Z
fulldoi: https://doi.org/10.1145/3658223
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '4'
keyword:
- surface tracking
- topology change
- non- manifold meshes
- multi-material flows
- solid modeling
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '19630'
relation: dissertation_contains
status: public
- id: '18301'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Multi-material mesh-based surface tracking with implicit topology changes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
OA_place: publisher
_id: '18301'
abstract:
- lang: eng
text: Physics simulation in computer graphics can bring triangle meshes into topologically
invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov*
et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker
that repairs explicit non-manifold triangle meshes with the help of the implicit
domain. Specifically, this thesis provides an algorithm for filling the holes
that are left after removing problematic parts of the mesh.
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Arian
full_name: Etemadihaghighi, Arian
id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f
last_name: Etemadihaghighi
citation:
ama: Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit
topology changes in surface tracking. 2024. doi:10.15479/at:ista:18301
apa: Etemadi, A. (2024). Filling the holes of non-manifold self-intersecting
meshes for implicit topology changes in surface tracking. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:18301
chicago: Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes
for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18301.
ieee: A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for
implicit topology changes in surface tracking,” Institute of Science and Technology
Austria, 2024.
ista: Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes
for implicit topology changes in surface tracking. Institute of Science and Technology
Austria.
mla: Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes
for Implicit Topology Changes in Surface Tracking. Institute of Science and
Technology Austria, 2024, doi:10.15479/at:ista:18301.
short: A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for
Implicit Topology Changes in Surface Tracking, Institute of Science and Technology
Austria, 2024.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-10-11T19:52:20Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2026-10-02T11:19:26Z
day: '15'
ddc:
- '000'
degree_awarded: MS
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/at:ista:18301
doi_confirm: '1'
file:
- access_level: open_access
checksum: 80fb7923e229ad9d39253d7c8a8083d0
content_type: application/pdf
creator: aetemadi
date_created: 2024-10-24T14:34:42Z
date_updated: 2024-10-24T14:34:42Z
file_id: '18469'
file_name: thesis-arian-etemadi.pdf
file_size: 8914218
relation: main_file
success: 1
- access_level: closed
checksum: 1c02586ed7d441d5ec441867650568d1
content_type: application/x-zip-compressed
creator: aetemadi
date_created: 2024-10-24T14:34:54Z
date_updated: 2024-10-24T14:34:54Z
file_id: '18470'
file_name: thesis-arian-etemadi-latex-source.zip
file_size: 9802650
relation: source_file
file_date_updated: 2024-10-24T14:34:54Z
fulldoi: https://doi.org/10.15479/at:ista:18301
has_accepted_license: '1'
keyword:
- surface tracking
- non-manifold
- hole-filling
- topology change
- multi-material
- solid-modeling
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: '39'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17219'
relation: part_of_dissertation
status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
supplementarymaterial: no
title: Filling the holes of non-manifold self-intersecting meshes for implicit topology
changes in surface tracking
tmp:
image: /images/cc_by_sa.png
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: dissertation
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '12178'
abstract:
- lang: eng
text: In this paper we consider the stochastic primitive equation for geophysical
flows subject to transport noise and turbulent pressure. Admitting very rough
noise terms, the global existence and uniqueness of solutions to this stochastic
partial differential equation are proven using stochastic maximal L² regularity,
the theory of critical spaces for stochastic evolution equations, and global a
priori bounds. Compared to other results in this direction, we do not need any
smallness assumption on the transport noise which acts directly on the velocity
field and we also allow rougher noise terms. The adaptation to Stratonovich type
noise and, more generally, to variable viscosity and/or conductivity are discussed
as well.
acknowledgement: The authors thank the anonymous referees for their helpful comments
and suggestions. Open Access funding enabled and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Matthias
full_name: Hieber, Matthias
last_name: Hieber
- first_name: Amru
full_name: Hussein, Amru
last_name: Hussein
- first_name: Martin
full_name: Saal, Martin
last_name: Saal
citation:
ama: 'Agresti A, Hieber M, Hussein A, Saal M. The stochastic primitive equations
with transport noise and turbulent pressure. Stochastics and Partial Differential
Equations: Analysis and Computations. 2024;12:53-133. doi:10.1007/s40072-022-00277-3'
apa: 'Agresti, A., Hieber, M., Hussein, A., & Saal, M. (2024). The stochastic
primitive equations with transport noise and turbulent pressure. Stochastics
and Partial Differential Equations: Analysis and Computations. Springer Nature.
https://doi.org/10.1007/s40072-022-00277-3'
chicago: 'Agresti, Antonio, Matthias Hieber, Amru Hussein, and Martin Saal. “The
Stochastic Primitive Equations with Transport Noise and Turbulent Pressure.” Stochastics
and Partial Differential Equations: Analysis and Computations. Springer Nature,
2024. https://doi.org/10.1007/s40072-022-00277-3.'
ieee: 'A. Agresti, M. Hieber, A. Hussein, and M. Saal, “The stochastic primitive
equations with transport noise and turbulent pressure,” Stochastics and Partial
Differential Equations: Analysis and Computations, vol. 12. Springer Nature,
pp. 53–133, 2024.'
ista: 'Agresti A, Hieber M, Hussein A, Saal M. 2024. The stochastic primitive equations
with transport noise and turbulent pressure. Stochastics and Partial Differential
Equations: Analysis and Computations. 12, 53–133.'
mla: 'Agresti, Antonio, et al. “The Stochastic Primitive Equations with Transport
Noise and Turbulent Pressure.” Stochastics and Partial Differential Equations:
Analysis and Computations, vol. 12, Springer Nature, 2024, pp. 53–133, doi:10.1007/s40072-022-00277-3.'
short: 'A. Agresti, M. Hieber, A. Hussein, M. Saal, Stochastics and Partial Differential
Equations: Analysis and Computations 12 (2024) 53–133.'
das_tickbox: '1'
dataavailabilitystatement: This manuscript has no associated data.
date_created: 2023-01-12T12:12:29Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-15T09:44:54Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s40072-022-00277-3
external_id:
arxiv:
- '2109.09561'
isi:
- '000874389000001'
file:
- access_level: open_access
checksum: 59c9000761134d681bdf9d482664044c
content_type: application/pdf
creator: dernst
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date_updated: 2024-07-22T09:29:48Z
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intvolume: ' 12'
isi: 1
keyword:
- Applied Mathematics
- Modeling and Simulation
- Statistics and Probability
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 53-133
publication: 'Stochastics and Partial Differential Equations: Analysis and Computations'
publication_identifier:
eissn:
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issn:
- 2194-0401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: yes
title: The stochastic primitive equations with transport noise and turbulent pressure
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2024'
...
---
_id: '12945'
abstract:
- lang: eng
text: "basic data for use in code for experimental data analysis for manuscript
under revision: \r\nDynamic pathogen detection and social feedback shape collective
hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S"
acknowledged_ssus:
- _id: LifeSc
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the
Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program
(Grant No. RGP0065/2012) to GT.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape
collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945'
apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback
shape collective hygiene in ants” . Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:12945'
chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:12945.'
ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape
collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.'
ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback
shape collective hygiene in ants’ , Institute of Science and Technology Austria,
10.15479/AT:ISTA:12945.'
mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria,
2023, doi:10.15479/AT:ISTA:12945.'
short: S. Cremer, (2023).
contributor:
- contributor_type: data_collector
first_name: Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- contributor_type: data_collector
first_name: Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- contributor_type: researcher
first_name: Katarina
last_name: Bodova
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
corr_author: '1'
date_created: 2023-05-11T21:35:17Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '12'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:12945
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creator: scremer
date_created: 2023-05-12T08:04:04Z
date_updated: 2023-05-12T08:04:04Z
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file_size: 3414674
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creator: scremer
date_created: 2023-05-12T08:04:08Z
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file_id: '12948'
file_name: README_Experimental_Data.md
file_size: 2113
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success: 1
file_date_updated: 2023-05-12T08:04:08Z
fulldoi: https://doi.org/10.15479/AT:ISTA:12945
has_accepted_license: '1'
keyword:
- collective behavior
- host-pathogen interactions
- social immunity
- epidemiology
- social insects
- probabilistic modeling
month: '05'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13127'
relation: used_in_publication
status: public
status: public
title: 'Data from: "Dynamic pathogen detection and social feedback shape collective
hygiene in ants" '
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12984'
abstract:
- lang: eng
text: Tattoos are a highly popular medium, with both artistic and medical applications.
Although the mechanical process of tattoo application has evolved historically,
the results are reliant on the artisanal skill of the artist. This can be especially
challenging for some skin tones, or in cases where artists lack experience. We
provide the first systematic overview of tattooing as a computational fabrication
technique. We built an automated tattooing rig and a recipe for the creation of
silicone sheets mimicking realistic skin tones, which allowed us to create an
accurate model predicting tattoo appearance. This enables several exciting applications
including tattoo previewing, color retargeting, novel ink spectra optimization,
color-accurate prosthetics, and more.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank Todor Asenov and the Miba Machine Shop for their help in
assembling the tattoo machine and manufacturing the substrates. We thank Geysler
Rodrigues for the insightful discussions on tattooing practices from a professional
artist's perspective. We thank Maria Fernanda Portugal for sharing a doctor's perspective
on medical applications of tattoos. This work is graciously supported by the FWF
Lise Meitner (Grant M 3319).
article_number: '67'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Alexandre
full_name: Chapiro, Alexandre
last_name: Chapiro
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Piovarci M, Chapiro A, Bickel B. Skin-Screen: A computational fabrication
framework for color tattoos. ACM Transactions on Graphics. 2023;42(4).
doi:10.1145/3592432'
apa: 'Piovarci, M., Chapiro, A., & Bickel, B. (2023). Skin-Screen: A computational
fabrication framework for color tattoos. ACM Transactions on Graphics.
Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592432'
chicago: 'Piovarci, Michael, Alexandre Chapiro, and Bernd Bickel. “Skin-Screen:
A Computational Fabrication Framework for Color Tattoos.” ACM Transactions
on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592432.'
ieee: 'M. Piovarci, A. Chapiro, and B. Bickel, “Skin-Screen: A computational fabrication
framework for color tattoos,” ACM Transactions on Graphics, vol. 42, no.
4. Association for Computing Machinery, 2023.'
ista: 'Piovarci M, Chapiro A, Bickel B. 2023. Skin-Screen: A computational fabrication
framework for color tattoos. ACM Transactions on Graphics. 42(4), 67.'
mla: 'Piovarci, Michael, et al. “Skin-Screen: A Computational Fabrication Framework
for Color Tattoos.” ACM Transactions on Graphics, vol. 42, no. 4, 67, Association
for Computing Machinery, 2023, doi:10.1145/3592432.'
short: M. Piovarci, A. Chapiro, B. Bickel, ACM Transactions on Graphics 42 (2023).
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
corr_author: '1'
date_created: 2023-05-16T09:39:14Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2025-04-15T07:43:53Z
day: '26'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3592432
external_id:
isi:
- '001044671300033'
file:
- access_level: open_access
checksum: 5f0a6867689e025a661bd0b4fd90b821
content_type: application/pdf
creator: mpiovarc
date_created: 2023-05-16T09:38:25Z
date_updated: 2023-05-16T09:38:25Z
file_id: '12985'
file_name: Piovarci2023.pdf
file_size: 30817343
relation: main_file
success: 1
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checksum: 6dd371de5b517e5f184f9c2cbea4b8b3
content_type: application/pdf
creator: dernst
date_created: 2024-04-16T05:52:18Z
date_updated: 2024-04-16T05:52:18Z
file_id: '15324'
file_name: 2023_ACM_Piovarci.pdf
file_size: 30281676
relation: main_file
success: 1
file_date_updated: 2024-04-16T05:52:18Z
fulldoi: https://doi.org/10.1145/3592432
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '4'
keyword:
- appearance
- modeling
- reproduction
- tattoo
- skin color
- gamut mapping
- ink-optimization
- prosthetic
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Skin-Screen: A computational fabrication framework for color tattoos'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14377'
abstract:
- lang: eng
text: Coherent flows of self-propelled particles are characterized by vortices and
jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal
a crossover between defect-free active turbulence and active turbulence laden
with topological defects. Interestingly, we show that concurrent to the crossover
from defect-free to defect-laden active turbulence is the restoration of the previously
broken SO(2) symmetry signaled by the fast decay of the two-point correlations.
By stability analyses of the topological charge density field, we provide theoretical
insights on the criterion for the crossover to the defect-laden active turbulent
state. Despite the distinct symmetry features between these two active turbulence
regimes, the flow fluctuations exhibit universal statistical scaling behaviors
at large scales, while the spectrum of polarity fluctuations decays exponentially
at small length scales compared to the active energy injection length. These findings
reveal a dynamical crossover between distinct spatiotemporal organization patterns
in polar active matter.
article_number: '063101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Benjamin H.
full_name: Andersen, Benjamin H.
last_name: Andersen
- first_name: Julian B
full_name: Renaud, Julian B
id: 7af6767d-14eb-11ed-b536-a32449ae867c
last_name: Renaud
- first_name: Jonas
full_name: Rønning, Jonas
last_name: Rønning
- first_name: Luiza
full_name: Angheluta, Luiza
last_name: Angheluta
- first_name: Amin
full_name: Doostmohammadi, Amin
last_name: Doostmohammadi
citation:
ama: Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. Symmetry-restoring
crossover from defect-free to defect-laden turbulence in polar active matter.
Physical Review Fluids. 2023;8(6). doi:10.1103/physrevfluids.8.063101
apa: Andersen, B. H., Renaud, J. B., Rønning, J., Angheluta, L., & Doostmohammadi,
A. (2023). Symmetry-restoring crossover from defect-free to defect-laden turbulence
in polar active matter. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/physrevfluids.8.063101
chicago: Andersen, Benjamin H., Julian B Renaud, Jonas Rønning, Luiza Angheluta,
and Amin Doostmohammadi. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden
Turbulence in Polar Active Matter.” Physical Review Fluids. American Physical
Society, 2023. https://doi.org/10.1103/physrevfluids.8.063101.
ieee: B. H. Andersen, J. B. Renaud, J. Rønning, L. Angheluta, and A. Doostmohammadi,
“Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar
active matter,” Physical Review Fluids, vol. 8, no. 6. American Physical
Society, 2023.
ista: Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. 2023. Symmetry-restoring
crossover from defect-free to defect-laden turbulence in polar active matter.
Physical Review Fluids. 8(6), 063101.
mla: Andersen, Benjamin H., et al. “Symmetry-Restoring Crossover from Defect-Free
to Defect-Laden Turbulence in Polar Active Matter.” Physical Review Fluids,
vol. 8, no. 6, 063101, American Physical Society, 2023, doi:10.1103/physrevfluids.8.063101.
short: B.H. Andersen, J.B. Renaud, J. Rønning, L. Angheluta, A. Doostmohammadi,
Physical Review Fluids 8 (2023).
date_created: 2023-09-29T08:46:47Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-10-03T07:25:39Z
day: '14'
doi: 10.1103/physrevfluids.8.063101
extern: '1'
external_id:
arxiv:
- '2209.10916'
fulldoi: https://doi.org/10.1103/physrevfluids.8.063101
intvolume: ' 8'
issue: '6'
keyword:
- Fluid Flow and Transfer Processes
- Modeling and Simulation
- Computational Mechanics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.10916
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_identifier:
issn:
- 2469-990X
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-restoring crossover from defect-free to defect-laden turbulence in
polar active matter
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14780'
abstract:
- lang: eng
text: In this paper, we study the eigenvalues and eigenvectors of the spiked invariant
multiplicative models when the randomness is from Haar matrices. We establish
the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩
for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence
rates. Moreover, we prove that the non-outlier eigenvalues stick with those of
the unspiked matrices and the non-outlier eigenvectors are delocalized. The results
also hold near the so-called BBP transition and for degenerate spikes. On one
hand, our results can be regarded as a refinement of the counterparts of [12]
under additional regularity conditions. On the other hand, they can be viewed
as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar
random matrix.
acknowledgement: The authors would like to thank the editor, the associated editor
and two anonymous referees for their many critical suggestions which have significantly
improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee
for many helpful discussions. The first author also wants to thank Hari Bercovici
for many useful comments. The first author is partially supported by National Science
Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant
“RMTBeyond” No. 101020331.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Xiucai
full_name: Ding, Xiucai
last_name: Ding
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Ding X, Ji HC. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009
apa: Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and
principal components. Stochastic Processes and Their Applications. Elsevier.
https://doi.org/10.1016/j.spa.2023.05.009
chicago: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices
and Principal Components.” Stochastic Processes and Their Applications.
Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009.
ieee: X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal
components,” Stochastic Processes and their Applications, vol. 163. Elsevier,
pp. 25–60, 2023.
ista: Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 163, 25–60.
mla: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and
Principal Components.” Stochastic Processes and Their Applications, vol.
163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.
short: X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023)
25–60.
date_created: 2024-01-10T09:29:25Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-07-16T08:01:03Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1016/j.spa.2023.05.009
ec_funded: 1
external_id:
arxiv:
- '2302.13502'
isi:
- '001113615900001'
file:
- access_level: open_access
checksum: 46a708b0cd5569a73d0f3d6c3e0a44dc
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:47:31Z
date_updated: 2024-01-16T08:47:31Z
file_id: '14806'
file_name: 2023_StochasticProcAppl_Ding.pdf
file_size: 1870349
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:47:31Z
fulldoi: https://doi.org/10.1016/j.spa.2023.05.009
has_accepted_license: '1'
intvolume: ' 163'
isi: 1
keyword:
- Applied Mathematics
- Modeling and Simulation
- Statistics and Probability
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 25-60
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Stochastic Processes and their Applications
publication_identifier:
eissn:
- 1879-209X
issn:
- 0304-4149
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spiked multiplicative random matrices and principal components
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 163
year: '2023'
...
---
_id: '13188'
abstract:
- lang: eng
text: "The Kirchhoff rod model describes the bending and twisting of slender elastic
rods in three dimensions, and has been widely studied to enable the prediction
of how a rod will deform, given its geometry and boundary conditions. In this
work, we study a number of inverse problems with the goal of computing the geometry
of a straight rod that will automatically deform to match a curved target shape
after attaching its endpoints to a support structure. Our solution lets us finely
control the static equilibrium state of a rod by varying the cross-sectional profiles
along its length.\r\nWe also show that the set of physically realizable equilibrium
states admits a concise geometric description in terms of linear line complexes,
which leads to very efficient computational design algorithms. Implemented in
an interactive software tool, they allow us to convert three-dimensional hand-drawn
spline curves to elastic rods, and give feedback about the feasibility and practicality
of a design in real time. We demonstrate the efficacy of our method by designing
and manufacturing several physical prototypes with applications to interior design
and soft robotics."
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank the anonymous reviewers for their generous feedback, and
Julian Fischer for his help in proving Proposition 1. This project has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No. 715767).
article_number: '171'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Hafner C, Bickel B. The design space of Kirchhoff rods. ACM Transactions
on Graphics. 2023;42(5). doi:10.1145/3606033
apa: Hafner, C., & Bickel, B. (2023). The design space of Kirchhoff rods. ACM
Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3606033
chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.”
ACM Transactions on Graphics. Association for Computing Machinery, 2023.
https://doi.org/10.1145/3606033.
ieee: C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” ACM Transactions
on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.
ista: Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions
on Graphics. 42(5), 171.
mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.”
ACM Transactions on Graphics, vol. 42, no. 5, 171, Association for Computing
Machinery, 2023, doi:10.1145/3606033.
short: C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).
corr_author: '1'
date_created: 2023-07-04T07:41:30Z
date_published: 2023-09-20T00:00:00Z
date_updated: 2026-10-26T23:30:05Z
day: '20'
ddc:
- '516'
department:
- _id: BeBi
doi: 10.1145/3606033
ec_funded: 1
external_id:
isi:
- '001086833300010'
file:
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creator: chafner
date_created: 2023-07-04T08:11:28Z
date_updated: 2023-07-04T08:11:28Z
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creator: chafner
date_created: 2023-07-04T07:46:28Z
date_updated: 2023-07-04T07:46:28Z
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file_size: 420909
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creator: chafner
date_created: 2023-07-04T07:46:30Z
date_updated: 2023-07-04T07:46:30Z
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title: Cheat Sheet for Notation
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creator: chafner
date_created: 2023-07-04T07:46:39Z
date_updated: 2023-07-04T07:46:39Z
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file_size: 268088064
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title: Supplemental Video
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creator: chafner
date_created: 2023-07-04T07:47:10Z
date_updated: 2023-07-04T07:47:10Z
file_id: '13193'
file_name: matlab-submission.zip
file_size: 25790
relation: supplementary_material
title: Matlab Source Code with Example
file_date_updated: 2023-07-04T08:11:28Z
fulldoi: https://doi.org/10.1145/3606033
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '5'
keyword:
- Computer Graphics
- Computational Design
- Computational Geometry
- Shape Modeling
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '12897'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: The design space of Kirchhoff rods
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '11556'
abstract:
- lang: eng
text: "We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation
kinetics and extend them for aggregation processes with collisional fragmentation
(shattering). We test the performance and accuracy of the extended methods and
compare their performance with efficient deterministic finite-difference method
applied to the same model. We validate the stochastic methods on the test problems
and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation
kinetics recently detected in deterministic simulations. We confirm the emergence
of steady oscillations of densities in such systems and prove the stability of
the\r\noscillations with respect to fluctuations and noise."
acknowledgement: Zhores supercomputer of Skolkovo Institute of Science and Technology
[68] has been used in the present research. S.A.M. was supported by Moscow Center
for Fundamental and Applied Mathematics (the agreement with the Ministry of Education
and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges
RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical
Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).
article_number: '111439'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: A.I.
full_name: Osinskiy, A.I.
last_name: Osinskiy
- first_name: S.A.
full_name: Matveev, S.A.
last_name: Matveev
- first_name: W.
full_name: Otieno, W.
last_name: Otieno
- first_name: N.V.
full_name: Brilliantov, N.V.
last_name: Brilliantov
citation:
ama: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation
Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal
of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439
apa: Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov,
N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439
chicago: Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov.
“Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.”
Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.
ieee: A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov,
“Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,”
Journal of Computational Physics, vol. 467. Elsevier, 2022.
ista: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct
simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics.
Journal of Computational Physics. 467, 111439.
mla: Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in
Aggregation-Fragmentation Kinetics.” Journal of Computational Physics,
vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.
short: A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal
of Computational Physics 467 (2022).
date_created: 2022-07-11T12:19:59Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2024-10-21T06:01:47Z
day: '15'
ddc:
- '518'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1016/j.jcp.2022.111439
external_id:
arxiv:
- '2103.09481'
isi:
- '000917225500013'
fulldoi: https://doi.org/10.1016/j.jcp.2022.111439
intvolume: ' 467'
isi: 1
keyword:
- Computer Science Applications
- Physics and Astronomy (miscellaneous)
- Applied Mathematics
- Computational Mathematics
- Modeling and Simulation
- Numerical Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.09481
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 467
year: '2022'
...
---
_id: '12145'
abstract:
- lang: eng
text: In the class of strictly convex smooth boundaries each of which has no strip
around its boundary foliated by invariant curves, we prove that the Taylor coefficients
of the “normalized” Mather’s β-function are invariant under C∞-conjugacies. In
contrast, we prove that any two elliptic billiard maps are C0-conjugate near their
respective boundaries, and C∞-conjugate, near the boundary and away from a line
passing through the center of the underlying ellipse. We also prove that, if the
billiard maps corresponding to two ellipses are topologically conjugate, then
the two ellipses are similar.
acknowledgement: "We are grateful to the anonymous referees for their careful reading
and valuable remarks and\r\ncomments which helped to improve the paper significantly.
We gratefully acknowledge support from the European Research Council (ERC) through
the Advanced Grant “SPERIG” (#885707)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Koudjinan E, Kaloshin V. On some invariants of Birkhoff billiards under conjugacy.
Regular and Chaotic Dynamics. 2022;27(6):525-537. doi:10.1134/S1560354722050021
apa: Koudjinan, E., & Kaloshin, V. (2022). On some invariants of Birkhoff billiards
under conjugacy. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/S1560354722050021
chicago: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff
Billiards under Conjugacy.” Regular and Chaotic Dynamics. Springer Nature,
2022. https://doi.org/10.1134/S1560354722050021.
ieee: E. Koudjinan and V. Kaloshin, “On some invariants of Birkhoff billiards under
conjugacy,” Regular and Chaotic Dynamics, vol. 27, no. 6. Springer Nature,
pp. 525–537, 2022.
ista: Koudjinan E, Kaloshin V. 2022. On some invariants of Birkhoff billiards under
conjugacy. Regular and Chaotic Dynamics. 27(6), 525–537.
mla: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards
under Conjugacy.” Regular and Chaotic Dynamics, vol. 27, no. 6, Springer
Nature, 2022, pp. 525–37, doi:10.1134/S1560354722050021.
short: E. Koudjinan, V. Kaloshin, Regular and Chaotic Dynamics 27 (2022) 525–537.
corr_author: '1'
date_created: 2023-01-12T12:06:49Z
date_published: 2022-10-03T00:00:00Z
date_updated: 2025-04-14T07:53:45Z
day: '03'
department:
- _id: VaKa
doi: 10.1134/S1560354722050021
ec_funded: 1
external_id:
arxiv:
- '2105.14640'
isi:
- '000865267300002'
fulldoi: https://doi.org/10.1134/S1560354722050021
intvolume: ' 27'
isi: 1
issue: '6'
keyword:
- Mechanical Engineering
- Applied Mathematics
- Mathematical Physics
- Modeling and Simulation
- Statistical and Nonlinear Physics
- Mathematics (miscellaneous)
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2105.14640
month: '10'
oa: 1
oa_version: Preprint
page: 525-537
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Regular and Chaotic Dynamics
publication_identifier:
eissn:
- 1468-4845
issn:
- 1560-3547
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1134/s1560354722060107
scopus_import: '1'
status: public
title: On some invariants of Birkhoff billiards under conjugacy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2022'
...
---
_id: '12152'
abstract:
- lang: eng
text: ESCRT-III filaments are composite cytoskeletal polymers that can constrict
and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III
filaments undergo a series of dramatic composition and geometry changes in the
presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the
membrane morphology. We set out to understand the physical mechanisms involved
in translating the changes in ESCRT-III polymer composition into membrane deformation.
We have built a coarse-grained model in which ESCRT-III polymers of different
geometries and mechanical properties are allowed to copolymerise and bind to a
deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific
polymers, we identify mechanical regimes in which changes in filament composition
trigger the associated membrane transition from a flat to a buckled state, and
then to a tubule state that eventually undergoes scission to release a small cargo-loaded
vesicle. We then characterise how the location and kinetics of polymer loss affects
the extent of membrane deformation and the efficiency of membrane neck scission.
Our results identify the near-minimal mechanical conditions for the operation
of shape-shifting composite polymers that sever membrane necks.
acknowledgement: "A.S . received an award from European Research Council (https://erc.europa.eu,
“NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org,
UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences
Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award
from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open,
Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an
award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation,
Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc,
MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research
(https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and
an award from the European Research Council\r\nConsolidator (https://erc.europa.eu,
311536). The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript."
article_number: e1010586
article_processing_charge: No
article_type: original
author:
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Elene
full_name: Lominadze, Elene
last_name: Lominadze
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane
reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational
Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586
apa: Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K.,
Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged
polymerization of ESCRT-III filaments. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1010586
chicago: Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos,
Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela
Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.”
PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.
ieee: X. Jiang et al., “Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public
Library of Science, 2022.
ista: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze
E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.
mla: Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization
of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.
short: X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E.
Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).
corr_author: '1'
date_created: 2023-01-12T12:08:10Z
date_published: 2022-10-17T00:00:00Z
date_updated: 2025-06-12T06:19:28Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1371/journal.pcbi.1010586
ec_funded: 1
external_id:
isi:
- '000924885500005'
pmid:
- '36251703'
file:
- access_level: open_access
checksum: bada6a7865e470cf42bbdfa67dd471d2
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:45:01Z
date_updated: 2023-01-24T10:45:01Z
file_id: '12359'
file_name: 2022_PLoSCompBio_Jiang.pdf
file_size: 2641067
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:45:01Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1010586
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '10'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
grant_number: '96752'
name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sharonJXY/3-filament-model
scopus_import: '1'
status: public
title: Modelling membrane reshaping by staged polymerization of ESCRT-III 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: 18
year: '2022'
...
---
_id: '12156'
abstract:
- lang: eng
text: Models of transcriptional regulation that assume equilibrium binding of transcription
factors have been less successful at predicting gene expression from sequence
in eukaryotes than in bacteria. This could be due to the non-equilibrium nature
of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium
mechanisms is vast and predominantly uninteresting. The key question is therefore
how this space can be navigated efficiently, to focus on mechanisms and models
that are biologically relevant. In this review, we advocate for the normative
role of theory—theory that prescribes rather than just describes—in providing
such a focus. Theory should expand its remit beyond inferring mechanistic models
from data, towards identifying non-equilibrium gene regulatory schemes that may
have been evolutionarily selected, despite their energy consumption, because they
are precise, reliable, fast, or otherwise outperform regulation at equilibrium.
We illustrate our reasoning by toy examples for which we provide simulation code.
acknowledgement: 'This work was supported through the Center for the Physics of Biological
Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and
U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant
FWF P28844 and the Human Frontiers Science Program. '
article_number: '100435'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or
non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
apa: Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation
at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435
chicago: Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation
at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier,
2022. https://doi.org/10.1016/j.coisb.2022.100435.
ieee: B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium,
or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier,
2022.
ista: Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium,
or non? Current Opinion in Systems Biology. 31(9), 100435.
mla: Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?”
Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022,
doi:10.1016/j.coisb.2022.100435.
short: B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
corr_author: '1'
date_created: 2023-01-12T12:08:51Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-06-11T13:47:43Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.coisb.2022.100435
external_id:
pmid:
- '36590072'
file:
- access_level: open_access
checksum: 97ef01e0cc60cdc84f45640a0f248fb0
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T12:14:10Z
date_updated: 2023-01-24T12:14:10Z
file_id: '12362'
file_name: 2022_CurrentBiology_Zoller.pdf
file_size: 2214944
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:14:10Z
fulldoi: https://doi.org/10.1016/j.coisb.2022.100435
has_accepted_license: '1'
intvolume: ' 31'
issue: '9'
keyword:
- Applied Mathematics
- Computer Science Applications
- Drug Discovery
- General Biochemistry
- Genetics and Molecular Biology
- Modeling and Simulation
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Current Opinion in Systems Biology
publication_identifier:
issn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eukaryotic gene regulation at equilibrium, or non?
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: 31
year: '2022'
...
---
_id: '12279'
abstract:
- lang: eng
text: We report frictional drag reduction and a complete flow relaminarization of
elastic turbulence (ET) at vanishing inertia in a viscoelastic channel flow past
an obstacle. We show that the intensity of the observed elastic waves and wall-normal
vorticity correlate well with the measured drag above the onset of ET. Moreover,
we find that the elastic wave frequency grows with the Weissenberg number, and
at sufficiently high frequency it causes a decay of the elastic waves, resulting
in ET attenuation and drag reduction. Thus, this allows us to substantiate a physical
mechanism, involving the interaction of elastic waves with wall-normal vorticity
fluctuations, leading to the drag reduction and relaminarization phenomena at
low Reynolds number.
acknowledgement: "We thank G. Falkovich for discussion and Guy Han for technical support.
We are grateful to N. Jha for his help in µPIV measurements. This work is partially
supported by the grants from\r\nIsrael Science Foundation (ISF; grant #882/15 and
grant #784/19) and Binational USA-Israel Foundation (BSF;grant #2016145). "
article_number: L081301
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M. Vijay
full_name: Kumar, M. Vijay
last_name: Kumar
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Dongyang
full_name: Li, Dongyang
last_name: Li
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Kumar MV, Varshney A, Li D, Steinberg V. Relaminarization of elastic turbulence.
Physical Review Fluids. 2022;7(8). doi:10.1103/physrevfluids.7.l081301
apa: Kumar, M. V., Varshney, A., Li, D., & Steinberg, V. (2022). Relaminarization
of elastic turbulence. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/physrevfluids.7.l081301
chicago: Kumar, M. Vijay, Atul Varshney, Dongyang Li, and Victor Steinberg. “Relaminarization
of Elastic Turbulence.” Physical Review Fluids. American Physical Society,
2022. https://doi.org/10.1103/physrevfluids.7.l081301.
ieee: M. V. Kumar, A. Varshney, D. Li, and V. Steinberg, “Relaminarization of elastic
turbulence,” Physical Review Fluids, vol. 7, no. 8. American Physical Society,
2022.
ista: Kumar MV, Varshney A, Li D, Steinberg V. 2022. Relaminarization of elastic
turbulence. Physical Review Fluids. 7(8), L081301.
mla: Kumar, M. Vijay, et al. “Relaminarization of Elastic Turbulence.” Physical
Review Fluids, vol. 7, no. 8, L081301, American Physical Society, 2022, doi:10.1103/physrevfluids.7.l081301.
short: M.V. Kumar, A. Varshney, D. Li, V. Steinberg, Physical Review Fluids 7 (2022).
corr_author: '1'
date_created: 2023-01-16T10:02:40Z
date_published: 2022-08-03T00:00:00Z
date_updated: 2024-10-09T21:03:55Z
day: '03'
department:
- _id: BjHo
doi: 10.1103/physrevfluids.7.l081301
external_id:
arxiv:
- '2205.12871'
isi:
- '000836397000001'
fulldoi: https://doi.org/10.1103/physrevfluids.7.l081301
intvolume: ' 7'
isi: 1
issue: '8'
keyword:
- Fluid Flow and Transfer Processes
- Modeling and Simulation
- Computational Mechanics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2205.12871'
month: '08'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_identifier:
issn:
- 2469-990X
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relaminarization of elastic turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2022'
...
---
_id: '12280'
abstract:
- lang: eng
text: 'In repeated interactions, players can use strategies that respond to the
outcome of previous rounds. Much of the existing literature on direct reciprocity
assumes that all competing individuals use the same strategy space. Here, we study
both learning and evolutionary dynamics of players that differ in the strategy
space they explore. We focus on the infinitely repeated donation game and compare
three natural strategy spaces: memory-1 strategies, which consider the last moves
of both players, reactive strategies, which respond to the last move of the co-player,
and unconditional strategies. These three strategy spaces differ in the memory
capacity that is needed. We compute the long term average payoff that is achieved
in a pairwise learning process. We find that smaller strategy spaces can dominate
larger ones. For weak selection, unconditional players dominate both reactive
and memory-1 players. For intermediate selection, reactive players dominate memory-1
players. Only for strong selection and low cost-to-benefit ratio, memory-1 players
dominate the others. We observe that the supergame between strategy spaces can
be a social dilemma: maximum payoff is achieved if both players explore a larger
strategy space, but smaller strategy spaces dominate.'
acknowledgement: "This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG
863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant
850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript."
article_number: e1010149
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals
that use different strategy spaces. PLOS Computational Biology. 2022;18(6).
doi:10.1371/journal.pcbi.1010149
apa: Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity
between individuals that use different strategy spaces. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149
chicago: Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak.
“Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS
Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149.
ieee: L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between
individuals that use different strategy spaces,” PLOS Computational Biology,
vol. 18, no. 6. Public Library of Science, 2022.
ista: Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between
individuals that use different strategy spaces. PLOS Computational Biology. 18(6),
e1010149.
mla: Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different
Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.
short: L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology
18 (2022).
corr_author: '1'
date_created: 2023-01-16T10:02:51Z
date_published: 2022-06-14T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1010149
ec_funded: 1
external_id:
isi:
- '000843626800031'
pmid:
- '35700167'
file:
- access_level: open_access
checksum: 31b6b311b6731f1658277a9dfff6632c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:28:13Z
date_updated: 2023-01-30T11:28:13Z
file_id: '12460'
file_name: 2022_PlosCompBio_Schmid.pdf
file_size: 3143222
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:28:13Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1010149
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '6'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLOS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reciprocity between individuals that use different strategy spaces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '9978'
abstract:
- lang: eng
text: Redox mediators could catalyse otherwise slow and energy-inefficient cycling
of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode
and the solid insulating storage materials. For mediators to work efficiently
they need to oxidize the solid with fast kinetics yet the lowest possible overpotential.
Here, we found that when the redox potentials of mediators are tuned via, e.g.,
Li + concentration in the electrolyte, they exhibit distinct threshold potentials,
where the kinetics accelerate several-fold within a range as small as 10 mV. This
phenomenon is independent of types of mediators and electrolyte. The acceleration
originates from the overpotentials required to activate fast Li + /e – extraction
and the following chemical step at specific abundant surface facets. Efficient
redox catalysis at insulating solids requires therefore carefully considering
the surface conditions of the storage materials and electrolyte-dependent redox
potentials, which may be tuned by salt concentrations or solvents.
acknowledgement: 'This work was financially supported by the National Natural Science
Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is
indebted to IST Austria for support. '
article_processing_charge: No
author:
- first_name: Deqing
full_name: Cao, Deqing
last_name: Cao
- first_name: Xiaoxiao
full_name: Shen, Xiaoxiao
last_name: Shen
- first_name: Aiping
full_name: Wang, Aiping
last_name: Wang
- first_name: Fengjiao
full_name: Yu, Fengjiao
last_name: Yu
- first_name: Yuping
full_name: Wu, Yuping
last_name: Wu
- first_name: Siqi
full_name: Shi, Siqi
last_name: Shi
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
citation:
ama: Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during
mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1
apa: Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp
kinetic acceleration potentials during mediated redox catalysis of insulators.
Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1
chicago: Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi,
Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials
during Mediated Redox Catalysis of Insulators.” Research Square. Research
Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.
ieee: D. Cao et al., “Sharp kinetic acceleration potentials during mediated
redox catalysis of insulators,” Research Square. Research Square.
ista: Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic
acceleration potentials during mediated redox catalysis of insulators. Research
Square, 10.21203/rs.3.rs-750965/v1.
mla: Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated
Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.
short: D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen,
Research Square (n.d.).
corr_author: '1'
date_created: 2021-08-31T12:54:16Z
date_published: 2021-08-18T00:00:00Z
date_updated: 2024-10-09T21:01:46Z
day: '18'
ddc:
- '541'
department:
- _id: StFr
doi: 10.21203/rs.3.rs-750965/v1
file:
- access_level: open_access
checksum: 1878e91c29d5769ed5a827b0b7addf00
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-31T14:02:19Z
date_updated: 2021-08-31T14:02:19Z
file_id: '9979'
file_name: 2021_ResearchSquare_Cao.pdf
file_size: 1019662
relation: main_file
success: 1
file_date_updated: 2021-08-31T14:02:19Z
fulldoi: https://doi.org/10.21203/rs.3.rs-750965/v1
has_accepted_license: '1'
keyword:
- Catalysis
- Energy engineering
- Materials theory and modeling
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
page: '21'
publication: Research Square
publication_identifier:
eissn:
- 2693-5015
publication_status: submitted
publisher: Research Square
related_material:
record:
- id: '10813'
relation: later_version
status: public
status: public
title: Sharp kinetic acceleration potentials during mediated redox catalysis of insulators
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...