---
_id: '15024'
abstract:
- lang: eng
text: Electrostatic correlations between ions dissolved in water are known to impact
their transport properties in numerous ways, from conductivity to ion selectivity.
The effects of these correlations on the solvent itself remain, however, much
less clear. In particular, the addition of salt has been consistently reported
to affect the solution’s viscosity, but most modeling attempts fail to reproduce
experimental data even at moderate salt concentrations. Here, we use an approach
based on stochastic density functional theory, which accurately captures charge
fluctuations and correlations. We derive a simple analytical expression for the
viscosity correction in concentrated electrolytes, by directly linking it to the
liquid’s structure factor. Our prediction compares quantitatively to experimental
data at all temperatures and all salt concentrations up to the saturation limit.
This universal link between the microscopic structure and viscosity allows us
to shed light on the nanoscale dynamics of water and ions under highly concentrated
and correlated conditions.
acknowledgement: The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu
Lizée for fruitful discussions. This project received funding from the European
Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 101034413.
article_number: '064503'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Paul
full_name: Robin, Paul
id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
last_name: Robin
orcid: 0000-0002-5728-9189
citation:
ama: Robin P. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215
apa: Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215
chicago: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.
ieee: P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,”
Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.
ista: Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes.
Journal of Chemical Physics. 160(6), 064503.
mla: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024,
doi:10.1063/5.0188215.
short: P. Robin, Journal of Chemical Physics 160 (2024).
date_created: 2024-02-25T23:00:55Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2024-02-27T08:16:06Z
day: '14'
ddc:
- '540'
department:
- _id: EdHa
doi: 10.1063/5.0188215
ec_funded: 1
external_id:
arxiv:
- '2311.11784'
pmid:
- '38349632'
file:
- access_level: open_access
checksum: 0a5e0ae70849bce674466fc054390ec0
content_type: application/pdf
creator: dernst
date_created: 2024-02-27T08:12:52Z
date_updated: 2024-02-27T08:12:52Z
file_id: '15034'
file_name: 2024_JourChemicalPhysics_Robin.pdf
file_size: 5452738
relation: main_file
success: 1
file_date_updated: 2024-02-27T08:12:52Z
has_accepted_license: '1'
intvolume: ' 160'
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 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: Correlation-induced viscous dissipation in concentrated 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: 160
year: '2024'
...
---
_id: '14321'
abstract:
- lang: eng
text: We demonstrate the possibility of a coupling between the magnetization direction
of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate
the mechanism of the coupling, we analyze a minimal Stoner model that includes
Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet.
The proposed mechanism allows us to study magnetic anisotropy of the system with
an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can
change magnetocrystalline anisotropy of the substrate. Our research aims to motivate
further experimental studies of the current-free chirality induced spin selectivity
effect involving both enantiomers.
acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan,
and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received
funding from the European Union’s Horizon Europe research and innovation program
under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot."
article_number: '104103'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet
can affect its magnetization direction. The Journal of Chemical Physics.
2023;159(10). doi:10.1063/5.0165806
apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral
dipoles on a ferromagnet can affect its magnetization direction. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806
chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev.
“Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The
Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.
ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles
on a ferromagnet can affect its magnetization direction,” The Journal of Chemical
Physics, vol. 159, no. 10. AIP Publishing, 2023.
ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on
a ferromagnet can affect its magnetization direction. The Journal of Chemical
Physics. 159(10), 104103.
mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its
Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no.
10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.
short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical
Physics 159 (2023).
date_created: 2023-09-13T09:25:09Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2023-09-20T09:48:12Z
day: '11'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0165806
ec_funded: 1
external_id:
arxiv:
- '2306.17592'
pmid:
- '37694742'
file:
- access_level: open_access
checksum: 507ab65ab29e2c987c94cabad7c5370b
content_type: application/pdf
creator: acappell
date_created: 2023-09-13T09:34:20Z
date_updated: 2023-09-13T09:34:20Z
file_id: '14322'
file_name: 104103_1_5.0165806.pdf
file_size: 5749653
relation: main_file
success: 1
file_date_updated: 2023-09-13T09:34:20Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '10'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7b5202-d553-11ed-ba76-9b1c1b258338
grant_number: '101062862'
name: Non-equilibrium Field Theory of Molecular Rotations
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
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: Achiral dipoles on a ferromagnet can affect its magnetization direction
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: 159
year: '2023'
...
---
_id: '14603'
abstract:
- lang: eng
text: Computing the solubility of crystals in a solvent using atomistic simulations
is notoriously challenging due to the complexities and convergence issues associated
with free-energy methods, as well as the slow equilibration in direct-coexistence
simulations. This paper introduces a molecular-dynamics workflow that simplifies
and robustly computes the solubility of molecular or ionic crystals. This method
is considerably more straightforward than the state-of-the-art, as we have streamlined
and optimised each step of the process. Specifically, we calculate the chemical
potential of the crystal using the gas-phase molecule as a reference state, and
employ the S0 method to determine the concentration dependence of the chemical
potential of the solute. We use this workflow to predict the solubilities of sodium
chloride in water, urea polymorphs in water, and paracetamol polymorphs in both
water and ethanol. Our findings indicate that the predicted solubility is sensitive
to the chosen potential energy surface. Furthermore, we note that the harmonic
approximation often fails for both molecular crystals and gas molecules at or
above room temperature, and that the assumption of an ideal solution becomes less
valid for highly soluble substances.
acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2
system operated by the University of Cambridge Research Computing Service funded
by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from
the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.
article_number: '184110'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Pin Yu
full_name: Chew, Pin Yu
last_name: Chew
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for
computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 2023;159(18). doi:10.1063/5.0173341
apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341
chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics
Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal
of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.
ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals,” Journal
of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.
ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 159(18), 184110.
mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing
Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics,
vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.
short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-14T00:00:00Z
date_updated: 2023-11-28T08:39:23Z
day: '14'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0173341
external_id:
arxiv:
- '2308.10886'
file:
- access_level: open_access
checksum: f668ee0d07096eef81159d05bc27aabc
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:39:06Z
date_updated: 2023-11-28T08:39:06Z
file_id: '14620'
file_name: 2023_JourChemicalPhysics_Reinhardt.pdf
file_size: 6276059
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:39:06Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '18'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '14619'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A streamlined molecular-dynamics workflow for computing solubilities of molecular
and ionic crystals
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: 159
year: '2023'
...
---
_id: '12705'
abstract:
- lang: eng
text: The elasticity of disordered and polydisperse polymer networks is a fundamental
problem of soft matter physics that is still open. Here, we self-assemble polymer
networks via simulations of a mixture of bivalent and tri- or tetravalent patchy
particles, which result in an exponential strand length distribution analogous
to that of experimental randomly cross-linked systems. After assembly, the network
connectivity and topology are frozen and the resulting system is characterized.
We find that the fractal structure of the network depends on the number density
at which the assembly has been carried out, but that systems with the same mean
valence and same assembly density have the same structural properties. Moreover,
we compute the long-time limit of the mean-squared displacement, also known as
the (squared) localization length, of the cross-links and of the middle monomers
of the strands, showing that the dynamics of long strands is well described by
the tube model. Finally, we find a relation connecting these two localization
lengths at high density and connect the cross-link localization length to the
shear modulus of the system.
acknowledgement: We thank Michael Lang for helpful discussions. We acknowledge financial
support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC)
and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir”
French Government program, managed by the French National Research Agency (ANR).
W.K. is a senior member of the Institut Universitaire de France.
article_number: '074905'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Andrea
full_name: Ninarello, Andrea
last_name: Ninarello
- first_name: José
full_name: Ruiz-Franco, José
last_name: Ruiz-Franco
- first_name: Virginie
full_name: Hugouvieux, Virginie
last_name: Hugouvieux
- first_name: Emanuela
full_name: Zaccarelli, Emanuela
last_name: Zaccarelli
- first_name: Cristian
full_name: Micheletti, Cristian
last_name: Micheletti
- first_name: Walter
full_name: Kob, Walter
last_name: Kob
- first_name: Lorenzo
full_name: Rovigatti, Lorenzo
last_name: Rovigatti
citation:
ama: Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of
model disordered, polydisperse, and defect-free polymer networks. Journal of
Chemical Physics. 2023;158(7). doi:10.1063/5.0134271
apa: Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli,
E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model
disordered, polydisperse, and defect-free polymer networks. Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271
chicago: Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux,
Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure
and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.”
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.
ieee: V. Sorichetti et al., “Structure and elasticity of model disordered,
polydisperse, and defect-free polymer networks,” Journal of Chemical Physics,
vol. 158, no. 7. American Institute of Physics, 2023.
ista: Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti
C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse,
and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.
mla: Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered,
Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics,
vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.
short: V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli,
C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).
date_created: 2023-03-05T23:01:05Z
date_published: 2023-02-21T00:00:00Z
date_updated: 2023-10-03T11:31:51Z
day: '21'
department:
- _id: AnSa
doi: 10.1063/5.0134271
external_id:
arxiv:
- '2211.04810'
isi:
- '000936943800002'
pmid:
- '36813705'
intvolume: ' 158'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04810
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and elasticity of model disordered, polydisperse, and defect-free
polymer networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 158
year: '2023'
...
---
_id: '12831'
abstract:
- lang: eng
text: The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations
of a many-body bath, can be used to describe an impurity rotating in a fluid or
solid environment. Here, we propose a coherent state ansatz in the co-rotating
frame, which provides a comprehensive theoretical description of angulons. We
reveal the quasiparticle properties, such as energies, quasiparticle weights,
and spectral functions, and show that our ansatz yields a persistent decrease
in the impurity’s rotational constant due to many-body dressing, which is consistent
with experimental observations. From our study, a picture of the angulon emerges
as an effective spin interacting with a magnetic field that is self-consistently
generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy,
which focuses on the response of rotating molecules to a laser perturbation in
the linear response regime. Importantly, we take into account initial-state interactions
that have been neglected in prior studies and reveal their impact on the excitation
spectrum. To examine the angulon instability regime, we use a single-excitation
ansatz and obtain results consistent with experiments, in which a broadening of
spectral lines is observed while phonon wings remain highly suppressed due to
initial-state interactions.
acknowledgement: We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt
for their valuable discussions. We acknowledge support by the Max Planck Society
and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC
2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges
support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
T.S. is supported by the National Key Research and Development Program of China
(Grant No. 2017YFA0718304) and the National Natural Science Foundation of China
(Grant Nos. 11974363, 12135018, and 12047503).
article_number: '134301'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Zhongda
full_name: Zeng, Zhongda
last_name: Zeng
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Tao
full_name: Shi, Tao
last_name: Shi
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
citation:
ama: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons
and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13).
doi:10.1063/5.0135893
apa: Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational
theory of angulons and their rotational spectroscopy. The Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893
chicago: Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard
Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893.
ieee: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory
of angulons and their rotational spectroscopy,” The Journal of Chemical Physics,
vol. 158, no. 13. American Institute of Physics, 2023.
ista: Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory
of angulons and their rotational spectroscopy. The Journal of Chemical Physics.
158(13), 134301.
mla: Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational
Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301,
American Institute of Physics, 2023, doi:10.1063/5.0135893.
short: Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical
Physics 158 (2023).
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-07T00:00:00Z
date_updated: 2023-08-01T14:08:47Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1063/5.0135893
ec_funded: 1
external_id:
arxiv:
- '2211.08070'
isi:
- '000970038800001'
file:
- access_level: open_access
checksum: 8d801babea4df48e08895c76571bb19e
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:28:38Z
date_updated: 2023-04-17T07:28:38Z
file_id: '12841'
file_name: 2023_JourChemicalPhysics_Zeng.pdf
file_size: 7388057
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:28:38Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '13'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variational theory of angulons and their rotational spectroscopy
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: 158
year: '2023'
...
---
_id: '12912'
abstract:
- lang: eng
text: The chemical potential of adsorbed or confined fluids provides insight into
their unique thermodynamic properties and determines adsorption isotherms. However,
it is often difficult to compute this quantity from atomistic simulations using
existing statistical mechanical methods. We introduce a computational framework
that utilizes static structure factors, thermodynamic integration, and free energy
perturbation for calculating the absolute chemical potential of fluids. For demonstration,
we apply the method to compute the adsorption isotherms of carbon dioxide in a
metal-organic framework and water in carbon nanotubes.
acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments
and suggestions on the article. B.C. acknowledges the resources provided by the
Cambridge Tier-2 system operated by the University of Cambridge Research Computing
Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.
article_number: '161101 '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rochus
full_name: Schmid, Rochus
last_name: Schmid
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids.
The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711
apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed
or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711
chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023.
https://doi.org/10.1063/5.0146711.
ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined
fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing,
2023.
ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined
fluids. The Journal of Chemical Physics. 158(16), 161101.
mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16,
161101, AIP Publishing, 2023, doi:10.1063/5.0146711.
short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-24T00:00:00Z
date_updated: 2023-08-01T14:34:49Z
day: '24'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0146711
external_id:
arxiv:
- '2302.01297'
isi:
- '001010676000010'
pmid:
- '37093149'
file:
- access_level: open_access
checksum: 4ab8c965f2fa4e17920bfa846847f137
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:44:49Z
date_updated: 2023-05-08T07:44:49Z
file_id: '12918'
file_name: 2023_JourChemicalPhysics_Schmid.pdf
file_size: 6499468
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:44:49Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/mu-adsorption
- relation: software
url: https://github.com/BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of adsorbed or confined fluids
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: 158
year: '2023'
...
---
_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).
date_created: 2022-05-22T17:04:48Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2023-09-05T11:59:00Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1063/5.0087769
ec_funded: 1
external_id:
isi:
- '000797236000004'
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
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'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 156
year: '2022'
...
---
_id: '12249'
abstract:
- lang: eng
text: 'The chemical potential of a component in a solution is defined as the free
energy change as the amount of that component changes. Computing this fundamental
thermodynamic property from atomistic simulations is notoriously difficult because
of the convergence issues involved in free energy methods and finite size effects.
This Communication presents the so-called S0 method, which can be used to obtain
chemical potentials from static structure factors computed from equilibrium molecular
dynamics simulations under the isothermal–isobaric ensemble. This new method is
demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures,
a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. '
acknowledgement: I thank Daan Frenkel for providing feedback on an early draft and
for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing
the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions
on the manuscript.
article_number: '121101'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 2022;157(12). doi:10.1063/5.0107059
apa: Cheng, B. (2022). Computing chemical potentials of solutions from structure
factors. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0107059
chicago: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0107059.
ieee: B. Cheng, “Computing chemical potentials of solutions from structure factors,”
The Journal of Chemical Physics, vol. 157, no. 12. AIP Publishing, 2022.
ista: Cheng B. 2022. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 157(12), 121101.
mla: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics, vol. 157, no. 12, 121101, AIP
Publishing, 2022, doi:10.1063/5.0107059.
short: B. Cheng, The Journal of Chemical Physics 157 (2022).
date_created: 2023-01-16T09:56:20Z
date_published: 2022-09-30T00:00:00Z
date_updated: 2023-08-04T09:43:11Z
day: '30'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0107059
external_id:
isi:
- '000862856000003'
file:
- access_level: open_access
checksum: b0915b706568a663a9a372fca24adf35
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:07:00Z
date_updated: 2023-01-30T09:07:00Z
file_id: '12441'
file_name: 2022_JourChemPhysics_Cheng.pdf
file_size: 4402384
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:07:00Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
issue: '12'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of solutions from structure factors
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: 157
year: '2022'
...
---
_id: '8587'
abstract:
- lang: eng
text: Inspired by the possibility to experimentally manipulate and enhance chemical
reactivity in helium nanodroplets, we investigate the effective interaction and
the resulting correlations between two diatomic molecules immersed in a bath of
bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle
describing two rotating molecules that align with respect to each other due to
the effective attractive interaction mediated by the excitations of the bath.
We study this system in different parameter regimes and apply several theoretical
approaches to describe its properties. Using a Born–Oppenheimer approximation,
we investigate the dependence of the effective intermolecular interaction on the
rotational state of the two molecules. In the strong-coupling regime, a product-state
ansatz shows that the molecules tend to have a strong alignment in the ground
state. To investigate the system in the weak-coupling regime, we apply a one-phonon
excitation variational ansatz, which allows us to access the energy spectrum.
In comparison to the angulon quasiparticle, the biangulon shows shifted angulon
instabilities and an additional spectral instability, where resonant angular momentum
transfer between the molecules and the bath takes place. These features are proposed
as an experimentally observable signature for the formation of the biangulon quasiparticle.
Finally, by using products of single angulon and bare impurity wave functions
as basis states, we introduce a diagonalization scheme that allows us to describe
the transition from two separated angulons to a biangulon as a function of the
distance between the two molecules.
acknowledgement: We are grateful to Areg Ghazaryan for valuable discussions. M.L.
acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27
and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No.
M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research
and innovation programme under the European Research Council (ERC) Grant Agreement
No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S.
was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
under Germany’s Excellence Strategy – EXC-2111 – 390814868.
article_number: '164302'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
citation:
ama: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular
forces and correlations mediated by a phonon bath. The Journal of Chemical
Physics. 2020;152(16). doi:10.1063/1.5144759
apa: Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert,
A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759
chicago: Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail
Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated
by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020.
https://doi.org/10.1063/1.5144759.
ieee: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert,
“Intermolecular forces and correlations mediated by a phonon bath,” The Journal
of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.
ista: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular
forces and correlations mediated by a phonon bath. The Journal of Chemical Physics.
152(16), 164302.
mla: Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon
Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing,
2020, doi:10.1063/1.5144759.
short: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The
Journal of Chemical Physics 152 (2020).
date_created: 2020-09-30T10:33:17Z
date_published: 2020-04-27T00:00:00Z
date_updated: 2024-08-07T07:16:53Z
day: '27'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1063/1.5144759
ec_funded: 1
external_id:
arxiv:
- '1912.02658'
isi:
- '000530448300001'
intvolume: ' 152'
isi: 1
issue: '16'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.02658
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '8958'
relation: dissertation_contains
status: public
status: public
title: Intermolecular forces and correlations mediated by a phonon bath
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 152
year: '2020'
...
---
_id: '9658'
abstract:
- lang: eng
text: Macroscopic models of nucleation provide powerful tools for understanding
activated phase transition processes. These models do not provide atomistic insights
and can thus sometimes lack material-specific descriptions. Here, we provide a
comprehensive framework for constructing a continuum picture from an atomistic
simulation of homogeneous nucleation. We use this framework to determine the equilibrium
shape of the solid nucleus that forms inside bulk liquid for a Lennard-Jones potential.
From this shape, we then extract the anisotropy of the solid-liquid interfacial
free energy, by performing a reverse Wulff construction in the space of spherical
harmonic expansions. We find that the shape of the nucleus is nearly spherical
and that its anisotropy can be perfectly described using classical models.
article_number: '044103'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
citation:
ama: Cheng B, Ceriotti M, Tribello GA. Classical nucleation theory predicts the
shape of the nucleus in homogeneous solidification. The Journal of Chemical
Physics. 2020;152(4). doi:10.1063/1.5134461
apa: Cheng, B., Ceriotti, M., & Tribello, G. A. (2020). Classical nucleation
theory predicts the shape of the nucleus in homogeneous solidification. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5134461
chicago: Cheng, Bingqing, Michele Ceriotti, and Gareth A. Tribello. “Classical Nucleation
Theory Predicts the Shape of the Nucleus in Homogeneous Solidification.” The
Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5134461.
ieee: B. Cheng, M. Ceriotti, and G. A. Tribello, “Classical nucleation theory predicts
the shape of the nucleus in homogeneous solidification,” The Journal of Chemical
Physics, vol. 152, no. 4. AIP Publishing, 2020.
ista: Cheng B, Ceriotti M, Tribello GA. 2020. Classical nucleation theory predicts
the shape of the nucleus in homogeneous solidification. The Journal of Chemical
Physics. 152(4), 044103.
mla: Cheng, Bingqing, et al. “Classical Nucleation Theory Predicts the Shape of
the Nucleus in Homogeneous Solidification.” The Journal of Chemical Physics,
vol. 152, no. 4, 044103, AIP Publishing, 2020, doi:10.1063/1.5134461.
short: B. Cheng, M. Ceriotti, G.A. Tribello, The Journal of Chemical Physics 152
(2020).
date_created: 2021-07-15T07:22:24Z
date_published: 2020-01-31T00:00:00Z
date_updated: 2023-02-23T14:03:55Z
day: '31'
doi: 10.1063/1.5134461
extern: '1'
external_id:
arxiv:
- '1910.13481'
pmid:
- '32007057'
intvolume: ' 152'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/classical-nucleation-theory-predicts-the-shape-of-the-nucleus-in-homogeneous-solidification(56af848b-eee8-4e9b-93cf-667373e4a49b).html
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
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: Classical nucleation theory predicts the shape of the nucleus in homogeneous
solidification
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 152
year: '2020'
...
---
_id: '7422'
abstract:
- lang: eng
text: Biochemical reactions often occur at low copy numbers but at once in crowded
and diverse environments. Space and stochasticity therefore play an essential
role in biochemical networks. Spatial-stochastic simulations have become a prominent
tool for understanding how stochasticity at the microscopic level influences the
macroscopic behavior of such systems. While particle-based models guarantee the
level of detail necessary to accurately describe the microscopic dynamics at very
low copy numbers, the algorithms used to simulate them typically imply trade-offs
between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s
Function Reaction Dynamics) is an exact algorithm that evades such trade-offs
by partitioning the N-particle system into M ≤ N analytically tractable one- and
two-particle systems; the analytical solutions (Green’s functions) then are used
to implement an event-driven particle-based scheme that allows particles to make
large jumps in time and space while retaining access to their state variables
at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that
implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based
simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on
2D planes representing membranes, and on 1D elongated cylinders representative
of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion
used to model active transport. We find that, for low particle densities, eGFRD2
is up to 6 orders of magnitude faster than conventional Brownian dynamics. We
exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1
gradient formation, which involves 3D diffusion, active transport on microtubules,
and autophosphorylation on the membrane, confirming recent experimental and theoretical
results on this system to hold under genuinely stochastic conditions.
article_number: '054108'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Joris
full_name: Paijmans, Joris
last_name: Paijmans
- first_name: Laurens
full_name: Bossen, Laurens
last_name: Bossen
- first_name: Thomas
full_name: Miedema, Thomas
last_name: Miedema
- first_name: Martijn
full_name: Wehrens, Martijn
last_name: Wehrens
- first_name: Nils B.
full_name: Becker, Nils B.
last_name: Becker
- first_name: Kazunari
full_name: Kaizu, Kazunari
last_name: Kaizu
- first_name: Koichi
full_name: Takahashi, Koichi
last_name: Takahashi
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: Pieter Rein
full_name: ten Wolde, Pieter Rein
last_name: ten Wolde
citation:
ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The
Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker,
N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn
Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom,
and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal
of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu
K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal
of Chemical Physics. 150(5), 054108.
mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of
Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker,
K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics
150 (2019).
date_created: 2020-01-30T10:34:36Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-09-06T14:59:28Z
day: '07'
department:
- _id: GaTk
doi: 10.1063/1.5064867
external_id:
arxiv:
- '1708.09364'
isi:
- '000458109300009'
intvolume: ' 150'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.09364
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: eGFRD in all dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2019'
...
---
_id: '9659'
abstract:
- lang: eng
text: The curvature dependence of interfacial free energy, which is crucial in quantitatively
predicting nucleation kinetics and the stability of bubbles and droplets, is quantified
by the Tolman length δ. For solid-liquid interfaces, however, δ has never been
computed directly due to various theoretical and practical challenges. Here we
perform a direct evaluation of the Tolman length from atomistic simulations of
a solid-liquid planar interface in out-of-equilibrium conditions, by first computing
the surface tension from the amplitude of thermal capillary fluctuations of a
localized version of the Gibbs dividing surface and by then calculating how much
the surface energy changes when it is defined relative to the equimolar dividing
surface. We computed δ for a model potential, and found a good agreement with
the values indirectly inferred from nucleation simulations. The agreement not
only validates our approach but also suggests that the nucleation free energy
of the system can be perfectly described using classical nucleation theory if
the Tolman length is taken into account.
article_number: '231102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Ceriotti M. Communication: Computing the Tolman length for solid-liquid
interfaces. The Journal of Chemical Physics. 2018;148(23). doi:10.1063/1.5038396'
apa: 'Cheng, B., & Ceriotti, M. (2018). Communication: Computing the Tolman
length for solid-liquid interfaces. The Journal of Chemical Physics. AIP
Publishing. https://doi.org/10.1063/1.5038396'
chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman
Length for Solid-Liquid Interfaces.” The Journal of Chemical Physics. AIP
Publishing, 2018. https://doi.org/10.1063/1.5038396.'
ieee: 'B. Cheng and M. Ceriotti, “Communication: Computing the Tolman length for
solid-liquid interfaces,” The Journal of Chemical Physics, vol. 148, no.
23. AIP Publishing, 2018.'
ista: 'Cheng B, Ceriotti M. 2018. Communication: Computing the Tolman length for
solid-liquid interfaces. The Journal of Chemical Physics. 148(23), 231102.'
mla: 'Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman
Length for Solid-Liquid Interfaces.” The Journal of Chemical Physics, vol.
148, no. 23, 231102, AIP Publishing, 2018, doi:10.1063/1.5038396.'
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018).
date_created: 2021-07-15T07:51:42Z
date_published: 2018-06-21T00:00:00Z
date_updated: 2023-02-23T14:03:57Z
day: '21'
doi: 10.1063/1.5038396
extern: '1'
external_id:
arxiv:
- '1803.09140'
pmid:
- '29935495'
intvolume: ' 148'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/1.5038396
month: '06'
oa: 1
oa_version: Submitted Version
pmid: 1
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: 'Communication: Computing the Tolman length for solid-liquid interfaces'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 148
year: '2018'
...
---
_id: '14006'
abstract:
- lang: eng
text: We present a theoretical formalism for the calculation of attosecond delays
in molecular photoionization. It is shown how delays relevant to one-photon-ionization,
also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole
matrix elements provided by molecular quantum scattering theory. These results
are used to derive formulae for the delays measured by two-photon attosecond interferometry
based on an attosecond pulse train and a dressing femtosecond infrared pulse.
These effective delays are first expressed in the molecular frame where maximal
information about the molecular photoionization dynamics is available. The effects
of averaging over the emission direction of the electron and the molecular orientation
are introduced analytically. We illustrate this general formalism for the case
of two polyatomic molecules. N2O serves as an example of a polar linear molecule
characterized by complex photoionization dynamics resulting from the presence
of molecular shape resonances. H2O illustrates the case of a non-linear molecule
with comparably simple photoionization dynamics resulting from a flat continuum.
Our theory establishes the foundation for interpreting measurements of the photoionization
dynamics of all molecules by attosecond metrology.
article_number: '124306'
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Wörner HJ. Theory of attosecond delays in molecular photoionization.
The Journal of Chemical Physics. 2017;146(12). doi:10.1063/1.4977933
apa: Baykusheva, D. R., & Wörner, H. J. (2017). Theory of attosecond delays
in molecular photoionization. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4977933
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond
Delays in Molecular Photoionization.” The Journal of Chemical Physics.
AIP Publishing, 2017. https://doi.org/10.1063/1.4977933.
ieee: D. R. Baykusheva and H. J. Wörner, “Theory of attosecond delays in molecular
photoionization,” The Journal of Chemical Physics, vol. 146, no. 12. AIP
Publishing, 2017.
ista: Baykusheva DR, Wörner HJ. 2017. Theory of attosecond delays in molecular photoionization.
The Journal of Chemical Physics. 146(12), 124306.
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond
Delays in Molecular Photoionization.” The Journal of Chemical Physics,
vol. 146, no. 12, 124306, AIP Publishing, 2017, doi:10.1063/1.4977933.
short: D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (2017).
date_created: 2023-08-10T06:36:19Z
date_published: 2017-03-28T00:00:00Z
date_updated: 2023-08-22T08:30:59Z
day: '28'
doi: 10.1063/1.4977933
extern: '1'
external_id:
pmid:
- '28388142'
intvolume: ' 146'
issue: '12'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '03'
oa_version: None
pmid: 1
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: Theory of attosecond delays in molecular photoionization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2017'
...
---
_id: '9660'
abstract:
- lang: eng
text: In this paper we discuss how the information contained in atomistic simulations
of homogeneous nucleation should be used when fitting the parameters in macroscopic
nucleation models. We show how the number of solid and liquid atoms in such simulations
can be determined unambiguously by using a Gibbs dividing surface and how the
free energy as a function of the number of solid atoms in the nucleus can thus
be extracted. We then show that the parameters (the chemical potential, the interfacial
free energy, and a Tolman correction) of a model based on classical nucleation
theory can be fitted using the information contained in these free-energy profiles
but that the parameters in such models are highly correlated. This correlation
is unfortunate as it ensures that small errors in the computed free energy surface
can give rise to large errors in the extrapolated properties of the fitted model.
To resolve this problem we thus propose a method for fitting macroscopic nucleation
models that uses simulations of planar interfaces and simulations of three-dimensional
nuclei in tandem. We show that when the chemical potentials and the interface
energy are pinned to their planar-interface values, more precise estimates for
the Tolman length are obtained. Extrapolating the free energy profile obtained
from small simulation boxes to larger nuclei is thus more reliable.
article_number: '104707'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation:
From atomistic nuclei to the planar limit. The Journal of Chemical Physics.
2017;147(10). doi:10.1063/1.4997180'
apa: 'Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy
of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180'
chicago: 'Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs
Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.”
The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.'
ieee: 'B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical
Physics, vol. 147, no. 10. AIP Publishing, 2017.'
ista: 'Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical
Physics. 147(10), 104707.'
mla: 'Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation:
From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics,
vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.'
short: B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147
(2017).
date_created: 2021-07-15T08:13:29Z
date_published: 2017-09-14T00:00:00Z
date_updated: 2023-02-23T14:04:02Z
day: '14'
doi: 10.1063/1.4997180
extern: '1'
external_id:
arxiv:
- '1703.06062'
pmid:
- '28915742'
intvolume: ' 147'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html
month: '09'
oa: 1
oa_version: Submitted Version
pmid: 1
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: 'The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to
the planar limit'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 147
year: '2017'
...
---
_id: '9661'
abstract:
- lang: eng
text: Macroscopic theories of nucleation such as classical nucleation theory envision
that clusters of the bulk stable phase form inside the bulk metastable phase.
Molecular dynamics simulations are often used to elucidate nucleation mechanisms,
by capturing the microscopic configurations of all the atoms. In this paper, we
introduce a thermodynamic model that links macroscopic theories and atomic-scale
simulations and thus provide a simple and elegant framework for testing the limits
of classical nucleation theory.
article_number: '034106'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models
of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3).
doi:10.1063/1.4973883
apa: Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and
macroscopic models of homogeneous nucleation. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/1.4973883
chicago: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883.
ieee: B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation,” The Journal of Chemical Physics, vol.
146, no. 3. AIP Publishing, 2017.
ista: Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.
mla: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).
date_created: 2021-07-15T08:27:31Z
date_published: 2017-01-21T00:00:00Z
date_updated: 2021-08-09T12:31:57Z
day: '21'
doi: 10.1063/1.4973883
extern: '1'
external_id:
arxiv:
- '1610.01322'
pmid:
- '28109231'
intvolume: ' 146'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01322
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
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: Bridging the gap between atomistic and macroscopic models of homogeneous nucleation
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 146
year: '2017'
...
---
_id: '10376'
abstract:
- lang: eng
text: Nucleation processes are at the heart of a large number of phenomena, from
cloud formation to protein crystallization. A recently emerging area where nucleation
is highly relevant is the initiation of filamentous protein self-assembly, a process
that has broad implications in many research areas ranging from medicine to nanotechnology.
As such, spontaneous nucleation of protein fibrils has received much attention
in recent years with many theoretical and experimental studies focusing on the
underlying physical principles. In this paper we make a step forward in this direction
and explore the early time behaviour of filamentous protein growth in the context
of nucleation theory. We first provide an overview of the thermodynamics and kinetics
of spontaneous nucleation of protein filaments in the presence of one relevant
degree of freedom, namely the cluster size. In this case, we review how key kinetic
observables, such as the reaction order of spontaneous nucleation, are directly
related to the physical size of the critical nucleus. We then focus on the increasingly
prominent case of filament nucleation that includes a conformational conversion
of the nucleating building-block as an additional slow step in the nucleation
process. Using computer simulations, we study the concentration dependence of
the nucleation rate. We find that, under these circumstances, the reaction order
of spontaneous nucleation with respect to the free monomer does no longer relate
to the overall physical size of the nucleating aggregate but rather to the portion
of the aggregate that actively participates in the conformational conversion.
Our results thus provide a novel interpretation of the common kinetic descriptors
of protein filament formation, including the reaction order of the nucleation
step or the scaling exponent of lag times, and put into perspective current theoretical
descriptions of protein aggregation.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss
National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences
Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.),
the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_number: '211926'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Alessio
full_name: Zaccone, Alessio
last_name: Zaccone
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous
filament nucleation via oligomers: Insights from theory and simulation. The
Journal of Chemical Physics. 2016;145(21). doi:10.1063/1.4965040'
apa: 'Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., & Frenkel,
D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights
from theory and simulation. The Journal of Chemical Physics. American Institute
of Physics. https://doi.org/10.1063/1.4965040'
chicago: 'Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles,
and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics.
American Institute of Physics, 2016. https://doi.org/10.1063/1.4965040.'
ieee: 'A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel,
“Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation,” The Journal of Chemical Physics, vol. 145, no. 21. American
Institute of Physics, 2016.'
ista: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics
of spontaneous filament nucleation via oligomers: Insights from theory and simulation.
The Journal of Chemical Physics. 145(21), 211926.'
mla: 'Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics,
vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:10.1063/1.4965040.'
short: A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal
of Chemical Physics 145 (2016).
date_created: 2021-11-29T10:01:57Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-11-29T10:33:11Z
day: '01'
doi: 10.1063/1.4965040
extern: '1'
external_id:
arxiv:
- '1610.02320'
pmid:
- '28799382'
intvolume: ' 145'
issue: '21'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02320
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 145
year: '2016'
...
---
_id: '10380'
abstract:
- lang: eng
text: Using non-equilibrium molecular dynamics simulations, it has been recently
demonstrated that water molecules align in response to an imposed temperature
gradient, resulting in an effective electric field. Here, we investigate how thermally
induced fields depend on the underlying treatment of long-ranged interactions.
For the short-ranged Wolf method and Ewald summation, we find the peak strength
of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient
of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower
than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139,
014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show
that this discrepancy can be traced back to the use of an incorrect kernel in
the calculation of the electrostatic field. More seriously, we find that the Wolf
method fails to predict correct molecular orientations, resulting in dipole densities
with opposite sign to those computed using Ewald summation. By considering two
different multipole expansions, we show that, for inhomogeneous polarisations,
the quadrupole contribution can be significant and even outweigh the dipole contribution
to the field. Finally, we propose a more accurate way of calculating the electrostatic
potential and the field. In particular, we show that averaging the microscopic
field analytically to obtain the macroscopic Maxwell field reduces the error bars
by up to an order of magnitude. As a consequence, the simulation times required
to reach a given statistical accuracy decrease by up to two orders of magnitude.
acknowledgement: The authors should like to dedicate this paper to the memory of Simon
de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations.
P.W. would like to thank the Austrian Academy of Sciences for financial support
through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop
in Zaragoza in May 2015, where these results were first presented. P.W. would also
like to thank Chao Zhang for pointing out the equivalence of the two expressions
for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the
importance of the quadrupole contribution in experimental studies of interfacial
systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago
groups for their advice. We further acknowledge support from the Federation of Austrian
Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan),
the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science
Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical
Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data
related to this publication are available at the University of Cambridge data repository
(http://dx.doi.org/10.17863/CAM.118).
article_number: '224102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: P.
full_name: Wirnsberger, P.
last_name: Wirnsberger
- first_name: D.
full_name: Fijan, D.
last_name: Fijan
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: M.
full_name: Neumann, M.
last_name: Neumann
- first_name: C.
full_name: Dellago, C.
last_name: Dellago
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 2016;144(22). doi:10.1063/1.4953036
apa: Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., & Frenkel,
D. (2016). Non-equilibrium simulations of thermally induced electric fields in
water. The Journal of Chemical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4953036
chicago: Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D.
Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in
Water.” The Journal of Chemical Physics. American Institute of Physics,
2016. https://doi.org/10.1063/1.4953036.
ieee: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel,
“Non-equilibrium simulations of thermally induced electric fields in water,” The
Journal of Chemical Physics, vol. 144, no. 22. American Institute of Physics,
2016.
ista: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 144(22), 224102.
mla: Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric
Fields in Water.” The Journal of Chemical Physics, vol. 144, no. 22, 224102,
American Institute of Physics, 2016, doi:10.1063/1.4953036.
short: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The
Journal of Chemical Physics 144 (2016).
date_created: 2021-11-29T11:08:52Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-11-29T13:09:08Z
day: '10'
doi: 10.1063/1.4953036
extern: '1'
external_id:
arxiv:
- '1602.02734'
pmid:
- '27305991'
intvolume: ' 144'
issue: '22'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02734
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium simulations of thermally induced electric fields in water
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 144
year: '2016'
...
---
_id: '14019'
abstract:
- lang: eng
text: The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized
three-membered-ring hydrocarbon. We report on a measurement of the high-resolution
photoelectron and photoionization spectra of cyclopropene and several deuterated
isotopomers, from which we have determined the rovibrational energy level structure
of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first
time. The synthesis of the partially deuterated isotopomers always resulted in
mixtures of several isotopomers, differing in their number of D atoms and in the
location of these atoms, so that the photoelectron spectra of deuterated samples
are superpositions of the spectra of several isotopomers. The rotationally resolved
spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state
of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave
numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon.
The analysis of the isotopic shifts of the vibrational levels enabled the assignment
of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺)
to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency
mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2
rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional
coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.
article_number: '064317'
article_processing_charge: No
article_type: original
author:
- first_name: K.
full_name: Vasilatou, K.
last_name: Vasilatou
- first_name: J. M.
full_name: Michaud, J. M.
last_name: Michaud
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: F.
full_name: Merkt, F.
last_name: Merkt
citation:
ama: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744'
apa: 'Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt,
F. (2014). The cyclopropene radical cation: Rovibrational level structure at low
energies from high-resolution photoelectron spectra. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.4890744'
chicago: 'Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi,
and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure
at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of
Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744.'
ieee: 'K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The
cyclopropene radical cation: Rovibrational level structure at low energies from
high-resolution photoelectron spectra,” The Journal of Chemical Physics,
vol. 141, no. 6. AIP Publishing, 2014.'
ista: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.'
mla: 'Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level
Structure at Low Energies from High-Resolution Photoelectron Spectra.” The
Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014,
doi:10.1063/1.4890744.'
short: K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal
of Chemical Physics 141 (2014).
date_created: 2023-08-10T06:38:30Z
date_published: 2014-08-14T00:00:00Z
date_updated: 2023-08-22T09:01:31Z
day: '14'
doi: 10.1063/1.4890744
extern: '1'
external_id:
pmid:
- '25134581'
intvolume: ' 141'
issue: '6'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
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: 'The cyclopropene radical cation: Rovibrational level structure at low energies
from high-resolution photoelectron spectra'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2014'
...
---
_id: '9662'
abstract:
- lang: eng
text: Fractionation of isotopes among distinct molecules or phases is a quantum
effect which is often exploited to obtain insights on reaction mechanisms, biochemical,
geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios
in atomistic simulations is challenging, because one needs to perform a thermodynamic
integration with respect to the isotope mass, along with time-consuming path integral
calculations. By re-formulating the problem as a particle exchange in the ring
polymer partition function, we derive new estimators giving direct access to the
differential partitioning of isotopes, which can simplify the calculations by
avoiding thermodynamic integration. We demonstrate the efficiency of these estimators
by applying them to investigate the isotope fractionation ratios in the gas-phase
Zundel cation, and in a few simple hydrocarbons.
article_number: '244112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293
apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope
fractionation ratios. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4904293
chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators
for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP
Publishing, 2014. https://doi.org/10.1063/1.4904293.
ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation
ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing,
2014.
ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 141(24), 244112.
mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for
Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141,
no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).
date_created: 2021-07-15T09:22:49Z
date_published: 2014-12-28T00:00:00Z
date_updated: 2021-08-09T12:32:24Z
day: '28'
doi: 10.1063/1.4904293
extern: '1'
external_id:
arxiv:
- '1412.1308'
pmid:
- '25554138'
intvolume: ' 141'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1308
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
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: Direct path integral estimators for isotope fractionation ratios
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 141
year: '2014'
...
---
_id: '9663'
abstract:
- lang: eng
text: 'Molecular dynamics simulations of small Cu nanoparticles using three different
interatomic potentials at rising temperature indicate that small nanoparticles
can undergo solid-solid structural transitions through a direct geometrical conversion
route. The direct geometrical conversion can happen for cuboctahedral nanoparticles,
which turn into an icosahedra shape: one diagonal of the square faces contracts,
and the faces are folded along the diagonal to give rise to two equilateral triangles.
The transition is a kinetic process that cannot be fully explained through an
energetic point of view. It has low activation energy and fast reaction time in
the simulations. The transition mechanism is via the transmission of shear waves
initiated from the particle surface and does not involve dislocation activity.'
article_number: '164314'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H. W.
full_name: Ngan, Alfonso H. W.
last_name: Ngan
citation:
ama: Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper
nanoparticles through direct geometrical conversion. The Journal of Chemical
Physics. 2013;138(16). doi:10.1063/1.4802025
apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural
transition of copper nanoparticles through direct geometrical conversion. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025
chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid
Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.”
The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025.
ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion,” The Journal
of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013.
ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion. The Journal of
Chemical Physics. 138(16), 164314.
mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural
Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The
Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013,
doi:10.1063/1.4802025.
short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).
date_created: 2021-07-15T09:27:58Z
date_published: 2013-04-28T00:00:00Z
date_updated: 2021-08-09T12:35:34Z
day: '28'
doi: 10.1063/1.4802025
extern: '1'
external_id:
pmid:
- '23635145'
intvolume: ' 138'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pubmed.ncbi.nlm.nih.gov/23635145/
month: '04'
oa: 1
oa_version: Submitted Version
pmid: 1
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: Thermally induced solid-solid structural transition of copper nanoparticles
through direct geometrical conversion
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 138
year: '2013'
...