---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21235'
abstract:
- lang: eng
text: The condensation of charged polymers is an important driver for the formation
of biomolecular condensates. Recent experiments suggest that this mechanism also
controls the clustering of eukaryotic chromosomes during the late stages of cell
division. In this process, interchromosome attraction is driven by the condensation
of cytoplasmic RNA and Ki-67, a charged intrinsically disordered protein that
coats the chromosomes as a brush. Attraction between chromosomes has been shown
to be specifically promoted by a localized charged patch on Ki-67, although the
physical mechanism remains unclear. To elucidate this process, we combine coarse-grained
simulations and analytical theory to study the RNA-mediated interaction between
charged polymer brushes on the chromosome surfaces. We show that the charged patch
on Ki-67 leads to interchromosome attraction via RNA bridging between the two
brushes, whereby the RNA preferentially interacts with the charged patches, leading
to stable, long-range forces. By contrast, if the brush is uniformly charged,
bridging is basically absent due to complete adsorption of RNA onto the brush.
Moreover, the RNA dynamics becomes caged in presence of the charged patch while
remaining diffusive with uniform charge. Our work sheds light on the physical
origin of chromosome clustering, while also suggesting a general mechanism for
cells to tune work production by biomolecular condensates via different charge
distributions.
acknowledgement: "This work was supported by the European Union’s Horizon 2020 research
and innovation programme (A.Š. and V.S., ERC grant Agreement No. 802960 to A.Š.,
I.P. and P.R.,\r\nMarie Skłodowska-Curie Grant Agreement No. 101034413), the German
Research Foundation (S.C-H. and A.H.-A., DFG Project No. 402723784 to S.C-H.), the
Vallee Scholarship\r\n(A.Š. and V.S.), the EMBO Young Investigator Programme (A.Š.),
and a Ph.D. fellowship from the Boehringer Ingelheim Fonds (A.H.-A.)."
article_number: '033010'
article_processing_charge: Yes
article_type: original
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Alberto
full_name: Hernandez-Armendariz, Alberto
last_name: Hernandez-Armendariz
- first_name: Sara
full_name: Cuylen-Haering, Sara
last_name: Cuylen-Haering
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S,
Šarić A. Charge distribution of the coating brush drives interchromosome attraction.
PRX Life. 2025;3(3). doi:10.1103/41fd-r847
apa: Sorichetti, V., Robin, P., Palaia, I., Hernandez-Armendariz, A., Cuylen-Haering,
S., & Šarić, A. (2025). Charge distribution of the coating brush drives interchromosome
attraction. PRX Life. American Physical Society. https://doi.org/10.1103/41fd-r847
chicago: Sorichetti, Valerio, Paul Robin, Ivan Palaia, Alberto Hernandez-Armendariz,
Sara Cuylen-Haering, and Anđela Šarić. “Charge Distribution of the Coating Brush
Drives Interchromosome Attraction.” PRX Life. American Physical Society,
2025. https://doi.org/10.1103/41fd-r847.
ieee: V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering,
and A. Šarić, “Charge distribution of the coating brush drives interchromosome
attraction,” PRX Life, vol. 3, no. 3. American Physical Society, 2025.
ista: Sorichetti V, Robin P, Palaia I, Hernandez-Armendariz A, Cuylen-Haering S,
Šarić A. 2025. Charge distribution of the coating brush drives interchromosome
attraction. PRX Life. 3(3), 033010.
mla: Sorichetti, Valerio, et al. “Charge Distribution of the Coating Brush Drives
Interchromosome Attraction.” PRX Life, vol. 3, no. 3, 033010, American
Physical Society, 2025, doi:10.1103/41fd-r847.
short: V. Sorichetti, P. Robin, I. Palaia, A. Hernandez-Armendariz, S. Cuylen-Haering,
A. Šarić, PRX Life 3 (2025).
corr_author: '1'
date_created: 2026-02-16T14:50:32Z
date_published: 2025-08-11T00:00:00Z
date_updated: 2026-02-17T11:16:26Z
day: '11'
ddc:
- '570'
department:
- _id: AnSa
- _id: EdHa
doi: 10.1103/41fd-r847
ec_funded: 1
file:
- access_level: open_access
checksum: 1702b9bdbfd902a7c08aa4f1479b390d
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T11:12:30Z
date_updated: 2026-02-17T11:12:30Z
file_id: '21287'
file_name: 2025_PRXLife_Sorichetti.pdf
file_size: 3732843
relation: main_file
success: 1
file_date_updated: 2026-02-17T11:12:30Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 349b6ff1-11ca-11ed-8bc3-f006047c2eeb
name: EMBO Young Investigator Program - Andela Saric
publication: PRX Life
publication_identifier:
eissn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Charge distribution of the coating brush drives interchromosome attraction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21256'
abstract:
- lang: eng
text: Collagen IV is one of the main components of the basement membrane, a layer
of material that lines the majority of tissues in multicellular organisms. Collagen
IV molecules assemble into networks, providing stiffness and elasticity to tissues
and informing cell and organ shape, especially during development. In this work,
we develop two coarse-grained models for collagen IV molecules that retain biochemical
bond specificity and coarse grain at different length scales. Through molecular-dynamics
simulations, we test the assembly and mechanics of the resulting networks and
measure their response to strain in terms of stress, microscopic alignment, and
bond dynamics. Within the basement membrane, collagen IV networks rearrange by
molecule turnover, which affects tissue organization and can be linked with enzyme
activity. Here we explore network rearrangements via bond remodeling, the process
of breaking and remaking of bonds between network molecules. We then investigate
the effects of active (enzymatic) bond remodeling. We find that this nonequilibrium
remodeling allows a network to keep its integrity under strain, while relaxing
fully over a variety of timescales, a dynamic response that is unavailable to
networks undergoing equilibrium remodeling.
acknowledgement: This work received funding from the European Research Council under
the European Union's Horizon 2020 research and innovation program through Grant
Agreement No. 802960 (B.M., V.S., I.P., and A.Š.), the European Union's Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 101034413 (I.P.), the NOMIS Foundation (F.P.-V.), the National Centre for the
Replacement, Refinement and Reduction of Animals in Research Grant No. NC/T002425/1
(N.K.), Leverhulme Trust project Grant No. RPG-2020-068 (N.K.), MRC Fellowship No.
MR/W027437/1 (Y.M.), a Lister Institute Research Prize (Y.M.) and EMBO Young Investigator
Programme (Y.M. and A.Š.).
article_number: '033019'
article_processing_charge: Yes
article_type: original
author:
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
orcid: 0000-0003-3441-1337
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Eryk
full_name: Ratajczyk, Eryk
last_name: Ratajczyk
- first_name: Fernanda L
full_name: Perez Verdugo, Fernanda L
id: 4ecec223-9070-11ef-a0a9-bc76077bea8d
last_name: Perez Verdugo
- first_name: Nargess
full_name: Khalilgharibi, Nargess
last_name: Khalilgharibi
- first_name: Yanlan
full_name: Mao, Yanlan
last_name: Mao
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Meadowcroft B, Sorichetti V, Ratajczyk E, et al. Nonequilibrium remodeling
of collagen IV networks in Silico. PRX Life. 2025;3. doi:10.1103/gdd5-rnh7
apa: Meadowcroft, B., Sorichetti, V., Ratajczyk, E., Perez Verdugo, F. L., Khalilgharibi,
N., Mao, Y., … Šarić, A. (2025). Nonequilibrium remodeling of collagen IV networks
in Silico. PRX Life. American Physical Society. https://doi.org/10.1103/gdd5-rnh7
chicago: Meadowcroft, Billie, Valerio Sorichetti, Eryk Ratajczyk, Fernanda L Perez
Verdugo, Nargess Khalilgharibi, Yanlan Mao, Ivan Palaia, and Anđela Šarić. “Nonequilibrium
Remodeling of Collagen IV Networks in Silico.” PRX Life. American Physical
Society, 2025. https://doi.org/10.1103/gdd5-rnh7.
ieee: B. Meadowcroft et al., “Nonequilibrium remodeling of collagen IV networks
in Silico,” PRX Life, vol. 3. American Physical Society, 2025.
ista: Meadowcroft B, Sorichetti V, Ratajczyk E, Perez Verdugo FL, Khalilgharibi
N, Mao Y, Palaia I, Šarić A. 2025. Nonequilibrium remodeling of collagen IV networks
in Silico. PRX Life. 3, 033019.
mla: Meadowcroft, Billie, et al. “Nonequilibrium Remodeling of Collagen IV Networks
in Silico.” PRX Life, vol. 3, 033019, American Physical Society, 2025,
doi:10.1103/gdd5-rnh7.
short: B. Meadowcroft, V. Sorichetti, E. Ratajczyk, F.L. Perez Verdugo, N. Khalilgharibi,
Y. Mao, I. Palaia, A. Šarić, PRX Life 3 (2025).
corr_author: '1'
date_created: 2026-02-16T15:55:03Z
date_published: 2025-09-05T00:00:00Z
date_updated: 2026-02-17T13:37:38Z
day: '05'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1103/gdd5-rnh7
ec_funded: 1
file:
- access_level: open_access
checksum: 04cae5231d97e533145c493880fadbd9
content_type: application/pdf
creator: dernst
date_created: 2026-02-17T13:36:01Z
date_updated: 2026-02-17T13:36:01Z
file_id: '21308'
file_name: 2025_PRXLife_Meadowcroft.pdf
file_size: 2277704
relation: main_file
success: 1
file_date_updated: 2026-02-17T13:36:01Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 349b6ff1-11ca-11ed-8bc3-f006047c2eeb
name: EMBO Young Investigator Program - Andela Saric
publication: PRX Life
publication_identifier:
eissn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Nonequilibrium remodeling of collagen IV networks in Silico
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20477'
abstract:
- lang: eng
text: An electric double-layer capacitor (EDLC) stores energy by modulating the
spatial distribution of ions in the electrolytic solution that it contains. We
determine the mean-field timescales for planar EDLC relaxation to equilibrium
after a potential difference is applied. We tackle first the fully symmetric case,
where positive and negative ionic species have the same valence and diffusivity,
and then the general, more complex, asymmetric case. Depending on the applied
voltage and salt concentration, different regimes appear, revealing a remarkably
rich phenomenology relevant for nanocapacitors.
acknowledgement: This work has received funding from the European Union’s Horizon
2020 and Horizon Europe research and innovation programs under the Marie Skłodowska-Curie
Grants No. 674979-NANOTRANS (I. P., P. B. W., B. R., E. T.), No. 101034413 (I. P.),
and No. 101119598-FLUXIONIC (M. D., B. R., E. T.), as well as from the European
Research Council under Grant No. 863473 (B. R.). B. R. acknowledges financial support
from the French Agence Nationale de la Recherche (ANR) under Grant No. ANR-21-CE29-0021-02
(DIADEM). I. P. thanks Anđela Šarić for further support at ISTA.
article_number: '148002'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Adelchi J.
full_name: Asta, Adelchi J.
last_name: Asta
- first_name: Megh
full_name: Dutta, Megh
last_name: Dutta
- first_name: Patrick B.
full_name: Warren, Patrick B.
last_name: Warren
- first_name: Benjamin
full_name: Rotenberg, Benjamin
last_name: Rotenberg
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. Charging dynamics
of electric double-layer nanocapacitors in mean field. Physical Review Letters.
2025;135(14). doi:10.1103/72b9-c8cq
apa: Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., & Trizac,
E. (2025). Charging dynamics of electric double-layer nanocapacitors in mean field.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/72b9-c8cq
chicago: Palaia, Ivan, Adelchi J. Asta, Megh Dutta, Patrick B. Warren, Benjamin
Rotenberg, and Emmanuel Trizac. “Charging Dynamics of Electric Double-Layer Nanocapacitors
in Mean Field.” Physical Review Letters. American Physical Society, 2025.
https://doi.org/10.1103/72b9-c8cq.
ieee: I. Palaia, A. J. Asta, M. Dutta, P. B. Warren, B. Rotenberg, and E. Trizac,
“Charging dynamics of electric double-layer nanocapacitors in mean field,” Physical
Review Letters, vol. 135, no. 14. American Physical Society, 2025.
ista: Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. 2025. Charging
dynamics of electric double-layer nanocapacitors in mean field. Physical Review
Letters. 135(14), 148002.
mla: Palaia, Ivan, et al. “Charging Dynamics of Electric Double-Layer Nanocapacitors
in Mean Field.” Physical Review Letters, vol. 135, no. 14, 148002, American
Physical Society, 2025, doi:10.1103/72b9-c8cq.
short: I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical
Review Letters 135 (2025).
corr_author: '1'
date_created: 2025-10-16T13:09:30Z
date_published: 2025-09-29T00:00:00Z
date_updated: 2025-12-01T15:02:16Z
day: '29'
ddc:
- '530'
department:
- _id: AnSa
doi: 10.1103/72b9-c8cq
ec_funded: 1
external_id:
arxiv:
- '2301.00610'
isi:
- '001587121300010'
file:
- access_level: open_access
checksum: e29809fea48b18217d1779980f7117c4
content_type: application/pdf
creator: dernst
date_created: 2025-10-23T11:57:20Z
date_updated: 2025-10-23T11:57:20Z
file_id: '20526'
file_name: 2025_PhysReviewLetters_Palaia.pdf
file_size: 480414
relation: main_file
success: 1
file_date_updated: 2025-10-23T11:57:20Z
has_accepted_license: '1'
intvolume: ' 135'
isi: 1
issue: '14'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Charging dynamics of electric double-layer nanocapacitors in mean field
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20483'
abstract:
- lang: eng
text: A parallel plate capacitor containing an electrolytic solution is the simplest
model of a supercapacitor or electric double-layer capacitor. Using both analytical
and numerical techniques, we solve the Poisson-Nernst-Planck equations for such
a system, describing the mean-field charging dynamics of the capacitor, when a
constant potential difference is abruptly applied to its plates. Working at constant
total number of ions, we focus on the physical processes involved in the relaxation
and, whenever possible, give its functional shape and exact time constants. We
first review and study the case of a symmetric binary electrolyte, where we assume
the two ionic species to have the same charges and diffusivities. We then relax
these assumptions and present results for a generic strong (i.e fully dissociated)
binary electrolyte. At low electrolyte concentration, the relaxation is simple
to understand, as the dynamics of positive and negative ions appear decoupled.
At higher electrolyte concentration, we distinguish several regimes. In the linear
regime (low voltages), relaxation is multiexponential, it starts by the buildup
of the equilibrium charge profile and continues with neutral mass diffusion, and
the relevant timescales feature both the average and the Nernst-Hartley diffusion
coefficients. In the purely nonlinear regime (intermediate voltages), the initial
relaxation is slowed down exponentially due to increased capacitance, while bulk
effects become more and more evident. In the fully nonlinear regime (high voltages),
the dynamics of charge and mass are completely entangled and, asymptotically,
the relaxation is linear in time. We finally discuss nonideal behavior in real
capacitors and provide conditions for which mean-field is expected to hold.
acknowledgement: This work has received funding from the European Union's Horizon
2020 and Horizon Europe research and innovation programs under the Marie Skłodowska-Curie
Grants No. 674979-NANOTRANS (I.P., P.B.W., B.R., and E.T.), No. 101034413 (I.P.),
and No. 101119598-FLUXIONIC (M.D., B.R., and E.T.), as well as from the European
Research Council under Grant No. 863473 (B.R.). B.R. acknowledges financial support
from the French Agence Nationale de la Recherche (ANR) under Grant No. ANR-21-CE29-0021-02
(DIADEM). I.P. thanks Anđela Šarić for further support at ISTA.
article_number: '035417'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Adelchi J.
full_name: Asta, Adelchi J.
last_name: Asta
- first_name: Megh
full_name: Dutta, Megh
last_name: Dutta
- first_name: Patrick B.
full_name: Warren, Patrick B.
last_name: Warren
- first_name: Benjamin
full_name: Rotenberg, Benjamin
last_name: Rotenberg
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: 'Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. Poisson-Nernst-Planck
charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric
binary electrolytes. Physical Review E. 2025;112(3). doi:10.1103/p4dg-snqf'
apa: 'Palaia, I., Asta, A. J., Dutta, M., Warren, P. B., Rotenberg, B., & Trizac,
E. (2025). Poisson-Nernst-Planck charging dynamics of an electric double-layer
capacitor: Symmetric and asymmetric binary electrolytes. Physical Review E.
American Physical Society. https://doi.org/10.1103/p4dg-snqf'
chicago: 'Palaia, Ivan, Adelchi J. Asta, Megh Dutta, Patrick B. Warren, Benjamin
Rotenberg, and Emmanuel Trizac. “Poisson-Nernst-Planck Charging Dynamics of an
Electric Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.”
Physical Review E. American Physical Society, 2025. https://doi.org/10.1103/p4dg-snqf.'
ieee: 'I. Palaia, A. J. Asta, M. Dutta, P. B. Warren, B. Rotenberg, and E. Trizac,
“Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor:
Symmetric and asymmetric binary electrolytes,” Physical Review E, vol.
112, no. 3. American Physical Society, 2025.'
ista: 'Palaia I, Asta AJ, Dutta M, Warren PB, Rotenberg B, Trizac E. 2025. Poisson-Nernst-Planck
charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric
binary electrolytes. Physical Review E. 112(3), 035417.'
mla: 'Palaia, Ivan, et al. “Poisson-Nernst-Planck Charging Dynamics of an Electric
Double-Layer Capacitor: Symmetric and Asymmetric Binary Electrolytes.” Physical
Review E, vol. 112, no. 3, 035417, American Physical Society, 2025, doi:10.1103/p4dg-snqf.'
short: I. Palaia, A.J. Asta, M. Dutta, P.B. Warren, B. Rotenberg, E. Trizac, Physical
Review E 112 (2025).
corr_author: '1'
date_created: 2025-10-16T13:15:16Z
date_published: 2025-09-29T00:00:00Z
date_updated: 2025-12-01T13:06:51Z
day: '29'
ddc:
- '530'
department:
- _id: AnSa
doi: 10.1103/p4dg-snqf
ec_funded: 1
external_id:
arxiv:
- '2303.07859'
isi:
- '001586173200001'
file:
- access_level: open_access
checksum: 658a9b1ce6b2edcf138b54c55a566f0e
content_type: application/pdf
creator: dernst
date_created: 2025-10-23T09:15:56Z
date_updated: 2025-10-23T09:15:56Z
file_id: '20521'
file_name: 2025_PhysReviewE_Palaia.pdf
file_size: 1211712
relation: main_file
success: 1
file_date_updated: 2025-10-23T09:15:56Z
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor:
Symmetric and asymmetric binary electrolytes'
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: 112
year: '2025'
...
---
_id: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- 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: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional colloidal aggregation in chiral bacterial baths
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '11340'
abstract:
- lang: eng
text: Like-charge attraction, driven by ionic correlations, challenges our understanding
of electrostatics both in soft and hard matter. For two charged planar surfaces
confining counterions and water, we prove that, even at relatively low correlation
strength, the relevant physics is the ground-state one, oblivious of fluctuations.
Based on this, we derive a simple and accurate interaction pressure that fulfills
known exact requirements and can be used as an effective potential. We test this
equation against implicit-solvent Monte Carlo simulations and against explicit-solvent
simulations of cement and several types of clays. We argue that water destructuring
under nanometric confinement drastically reduces dielectric screening, enhancing
ionic correlations. Our equation of state at reduced permittivity therefore explains
the exotic attractive regime reported for these materials, even in the absence
of multivalent counterions.
acknowledgement: We thank Martin Trulsson for useful discussions and for providing
us with simulation data. This work has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21
is acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Abhay
full_name: Goyal, Abhay
last_name: Goyal
- first_name: Emanuela
full_name: Del Gado, Emanuela
last_name: Del Gado
- first_name: Ladislav
full_name: Šamaj, Ladislav
last_name: Šamaj
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at
the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028'
apa: 'Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., & Trizac, E. (2022). Like-charge
attraction at the nanoscale: Ground-state correlations and water destructuring.
Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028'
chicago: 'Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel
Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and
Water Destructuring.” Journal of Physical Chemistry B. American Chemical
Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.'
ieee: 'I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring,” Journal
of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp.
3143–3149, 2022.'
ista: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 126(16), 3143–3149.'
mla: 'Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State
Correlations and Water Destructuring.” Journal of Physical Chemistry B,
vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.'
short: I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical
Chemistry B 126 (2022) 3143–3149.
date_created: 2022-05-01T22:01:42Z
date_published: 2022-04-14T00:00:00Z
date_updated: 2025-06-11T13:34:36Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
pmid:
- '35420420'
intvolume: ' 126'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2203.10524'
month: '04'
oa: 1
oa_version: Preprint
page: 3143-3149
pmid: 1
publication: Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Like-charge attraction at the nanoscale: Ground-state correlations and water
destructuring'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2022'
...
---
_id: '11400'
abstract:
- lang: eng
text: By varying the concentration of molecules in the cytoplasm or on the membrane,
cells can induce the formation of condensates and liquid droplets, similar to
phase separation. Their thermodynamics, much studied, depends on the mutual interactions
between microscopic constituents. Here, we focus on the kinetics and size control
of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids,
we model a system of two species of proteins, giving origin to specific heterotypic
bonds. We find that concentrations, together with valence and bond strength, control
both the size and the growth time rate of the clusters. In particular, if one
species is in large excess, it gradually saturates the binding sites of the other
species; the system then becomes kinetically arrested and cluster coarsening slows
down or stops, thus yielding effective size selection. This phenomenology is observed
both in solid and fluid clusters, which feature additional generic homotypic interactions
and are reminiscent of the ones observed on biological membranes.
acknowledgement: "The authors thank Longhui Zeng and Xiaolei Su (Yale University)
for bringing the topic to their attention and for useful comments. This work has
received funding from the European Research Council under the European Union’s Horizon\r\n2020
research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie
Grant No. 101034413). The authors are grateful to the UK Materials and Molecular
Modeling Hub for computational resources, which is partially funded by EPSRC (Grant
Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and
from the Royal Society (Grant No. UF160266)."
article_number: '194902'
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures
with specific interactions. The Journal of Chemical Physics. 2022;156(19).
doi:10.1063/5.0087769
apa: Palaia, I., & Šarić, A. (2022). Controlling cluster size in 2D phase-separating
binary mixtures with specific interactions. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/5.0087769
chicago: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics.
AIP Publishing, 2022. https://doi.org/10.1063/5.0087769.
ieee: I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions,” The Journal of Chemical Physics,
vol. 156, no. 19. AIP Publishing, 2022.
ista: Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions. The Journal of Chemical Physics. 156(19),
194902.
mla: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics,
vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:10.1063/5.0087769.
short: I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).
corr_author: '1'
date_created: 2022-05-22T17:04:48Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2025-06-11T14:00:32Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1063/5.0087769
ec_funded: 1
external_id:
isi:
- '000797236000004'
pmid:
- '35597653'
file:
- access_level: open_access
checksum: 7fada58059676a4bb0944b82247af740
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T07:45:33Z
date_updated: 2022-05-23T07:45:33Z
file_id: '11405'
file_name: 2022_JourChemPhysics_Palaia.pdf
file_size: 6387208
relation: main_file
success: 1
file_date_updated: 2022-05-23T07:45:33Z
has_accepted_license: '1'
intvolume: ' 156'
isi: 1
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '05'
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: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling cluster size in 2D phase-separating binary mixtures with specific
interactions
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
year: '2022'
...
---
_id: '12108'
abstract:
- lang: eng
text: The sequential exchange of filament composition to increase filament curvature
was proposed as a mechanism for how some biological polymers deform and cut membranes.
The relationship between the filament composition and its mechanical effect is
lacking. We develop a kinetic model for the assembly of composite filaments that
includes protein–membrane adhesion, filament mechanics and membrane mechanics.
We identify the physical conditions for such a membrane remodeling and show this
mechanism of sequential polymer assembly lowers the energetic barrier for membrane
deformation.
acknowledgement: "We thank T. C. T. Michaels and J. Palacci for useful discussions.
We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge
funding by the European Union’s Horizon 2020 Research and Innovation Programme under
the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society
Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P.,
and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). "
article_number: '268101'
article_processing_charge: No
article_type: original
author:
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
orcid: 0000-0003-3441-1337
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anna Katharina
full_name: Pfitzner, Anna Katharina
last_name: Pfitzner
- 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: Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical
rules for shape-shifting filaments that remodel membranes. Physical Review
Letters. 2022;129(26). doi:10.1103/PhysRevLett.129.268101
apa: Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., & Šarić,
A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.129.268101
chicago: Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux,
Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments
That Remodel Membranes.” Physical Review Letters. American Physical Society,
2022. https://doi.org/10.1103/PhysRevLett.129.268101.
ieee: B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić,
“Mechanochemical rules for shape-shifting filaments that remodel membranes,” Physical
Review Letters, vol. 129, no. 26. American Physical Society, 2022.
ista: Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical
rules for shape-shifting filaments that remodel membranes. Physical Review Letters.
129(26), 268101.
mla: Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments
That Remodel Membranes.” Physical Review Letters, vol. 129, no. 26, 268101,
American Physical Society, 2022, doi:10.1103/PhysRevLett.129.268101.
short: B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical
Review Letters 129 (2022).
corr_author: '1'
date_created: 2023-01-08T23:00:53Z
date_published: 2022-12-23T00:00:00Z
date_updated: 2025-04-14T07:54:53Z
day: '23'
department:
- _id: AnSa
doi: 10.1103/PhysRevLett.129.268101
ec_funded: 1
external_id:
isi:
- '000906721500001'
pmid:
- '36608212'
intvolume: ' 129'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2022.05.10.490642 '
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _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: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanochemical rules for shape-shifting filaments that remodel membranes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 129
year: '2022'
...