---
_id: '14831'
abstract:
- lang: eng
text: Catalysis, the acceleration of product formation by a substance that is left
unchanged, typically results from multiple elementary processes, including diffusion
of the reactants toward the catalyst, chemical steps, and release of the products.
While efforts to design catalysts are often focused on accelerating the chemical
reaction on the catalyst, catalysis is a global property of the catalytic cycle
that involves all processes. These are controlled by both intrinsic parameters
such as the composition and shape of the catalyst and extrinsic parameters such
as the concentration of the chemical species at play. We examine here the conditions
that catalysis imposes on the different steps of a reaction cycle and the respective
role of intrinsic and extrinsic parameters of the system on the emergence of catalysis
by using an approach based on first-passage times. We illustrate this approach
for various decompositions of a catalytic cycle into elementary steps, including
non-Markovian decompositions, which are useful when the presence and nature of
intermediate states are a priori unknown. Our examples cover different types of
reactions and clarify the constraints on elementary steps and the impact of species
concentrations on catalysis.
acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received
funding from the European Unions Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie grant agreement No. 754387.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yann
full_name: Sakref, Yann
last_name: Sakref
- first_name: Maitane
full_name: Muñoz Basagoiti, Maitane
id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
last_name: Muñoz Basagoiti
orcid: 0000-0003-1483-1457
- first_name: Zorana
full_name: Zeravcic, Zorana
last_name: Zeravcic
- first_name: Olivier
full_name: Rivoire, Olivier
last_name: Rivoire
citation:
ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627
apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On
kinetic constraints that catalysis imposes on elementary processes. The Journal
of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627
chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire.
“On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The
Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.
ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints
that catalysis imposes on elementary processes,” The Journal of Physical Chemistry
B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.
ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 127(51), 10950–10959.
mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary
Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American
Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.
short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical
Chemistry B 127 (2023) 10950–10959.
date_created: 2024-01-18T07:47:11Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-01-23T07:58:27Z
day: '13'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.3c04627
external_id:
arxiv:
- '2312.15940'
isi:
- '001134068000001'
intvolume: ' 127'
isi: 1
issue: '51'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2312.15940
month: '12'
oa: 1
oa_version: Preprint
page: 10950-10959
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: On kinetic constraints that catalysis imposes on elementary processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
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: 2023-08-03T06:42:50Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
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
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2022'
...
---
_id: '10357'
abstract:
- lang: eng
text: The misfolding and aggregation of proteins into linear fibrils is widespread
in human biology, for example, in connection with amyloid formation and the pathology
of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The
oligomeric species that are formed in the early stages of protein aggregation
are of great interest, having been linked with the cellular toxicity associated
with these conditions. However, these species are not characterized in any detail
experimentally, and their properties are not well understood. Many of these species
have been found to have approximately spherical morphology and to be held together
by hydrophobic interactions. We present here an analytical statistical mechanical
model of globular oligomer formation from simple idealized amphiphilic protein
monomers and show that this correlates well with Monte Carlo simulations of oligomer
formation. We identify the controlling parameters of the model, which are closely
related to simple quantities that may be fitted directly from experiment. We predict
that globular oligomers are unlikely to form at equilibrium in many polypeptide
systems but instead form transiently in the early stages of amyloid formation.
We contrast the globular model of oligomer formation to a well-established model
of linear oligomer formation, highlighting how the differing ensemble properties
of linear and globular oligomers offer a potential strategy for characterizing
oligomers from experimental measurements.
acknowledgement: We acknowledge support from the Schiff Foundation (A.J.D.), the Royal
Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse,
Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome
Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC
(T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research
leading to these results has received funding from the European Research Council
under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through
the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several
useful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J.
full_name: Dear, Alexander J.
last_name: Dear
- 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: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics
of globular oligomer formation by protein molecules. The Journal of Physical
Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805
apa: Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T.
P. J. (2018). Statistical mechanics of globular oligomer formation by protein
molecules. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/acs.jpcb.8b07805
chicago: Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M.
Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer
Formation by Protein Molecules.” The Journal of Physical Chemistry B. American
Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.
ieee: A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles,
“Statistical mechanics of globular oligomer formation by protein molecules,” The
Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society,
pp. 11721–11730, 2018.
ista: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical
mechanics of globular oligomer formation by protein molecules. The Journal of
Physical Chemistry B. 122(49), 11721–11730.
mla: Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation
by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no.
49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.
short: A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal
of Physical Chemistry B 122 (2018) 11721–11730.
date_created: 2021-11-26T11:55:12Z
date_published: 2018-10-18T00:00:00Z
date_updated: 2021-11-26T12:40:02Z
day: '18'
doi: 10.1021/acs.jpcb.8b07805
extern: '1'
external_id:
pmid:
- '30336667'
intvolume: ' 122'
issue: '49'
keyword:
- materials chemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 11721-11730
pmid: 1
publication: The 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: Statistical mechanics of globular oligomer formation by protein molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 122
year: '2018'
...
---
_id: '8453'
abstract:
- lang: eng
text: Transverse relaxation rate measurements in magic-angle spinning solid-state
nuclear magnetic resonance provide information about molecular motions occurring
on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear
(13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency
field (R1ρ relaxation) provides access to such motions, and an increasing number
of studies involving R1ρ relaxation in proteins have been reported. However, two
factors that influence the observed relaxation rate constants have so far been
neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR)
and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and
relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that
the CCR rate constant depends on ns–ms motions; it can thus provide insight into
dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling
effect on the doublet components. For measurements of dynamics, the use of R1ρ
rate constants has practical advantages over the use of CCR rates, and this article
reveals factors that have so far been disregarded and which are important for
accurate measurements and interpretation.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Emmanuelle
full_name: Weber, Emmanuelle
last_name: Weber
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 2016;120(34):8905-8913. doi:10.1021/acs.jpcb.6b06129'
apa: 'Kurauskas, V., Weber, E., Hessel, A., Ayala, I., Marion, D., & Schanda,
P. (2016). Cross-correlated relaxation of dipolar coupling and chemical-shift
anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein
backbone dynamics measurements. The Journal of Physical Chemistry B. American
Chemical Society. https://doi.org/10.1021/acs.jpcb.6b06129'
chicago: 'Kurauskas, Vilius, Emmanuelle Weber, Audrey Hessel, Isabel Ayala, Dominique
Marion, and Paul Schanda. “Cross-Correlated Relaxation of Dipolar Coupling and
Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcb.6b06129.'
ieee: 'V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, and P. Schanda, “Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements,”
The Journal of Physical Chemistry B, vol. 120, no. 34. American Chemical
Society, pp. 8905–8913, 2016.'
ista: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. 2016. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 120(34), 8905–8913.'
mla: 'Kurauskas, Vilius, et al. “Cross-Correlated Relaxation of Dipolar Coupling
and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B, vol. 120, no. 34, American Chemical Society, 2016, pp. 8905–13, doi:10.1021/acs.jpcb.6b06129.'
short: V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, P. Schanda, The Journal
of Physical Chemistry B 120 (2016) 8905–8913.
date_created: 2020-09-18T10:07:07Z
date_published: 2016-08-08T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '08'
doi: 10.1021/acs.jpcb.6b06129
extern: '1'
intvolume: ' 120'
issue: '34'
keyword:
- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces
- Coatings and Films
language:
- iso: eng
month: '08'
oa_version: None
page: 8905-8913
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy
in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics
measurements'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2016'
...
---
_id: '10390'
abstract:
- lang: eng
text: 'We use numerical simulations to study the phase behavior of a system of purely
repulsive soft dumbbells as a function of size ratio of the two components and
their relative degree of deformability. We find a plethora of different phases,
which includes most of the mesophases observed in self-assembly of block copolymers
but also crystalline structures formed by asymmetric, hard binary mixtures. Our
results detail the phenomenological behavior of these systems when softness is
introduced in terms of two different classes of interparticle interactions: (a)
the elastic Hertz potential, which has a finite energy cost for complete overlap
of any two components, and (b) a generic power-law repulsion with tunable exponent.
We discuss how simple geometric arguments can be used to account for the large
structural variety observed in these systems and detail the similarities and differences
in the phase behavior for the two classes of potentials under consideration.'
acknowledgement: This work was supported by the National Science Foundation under
CAREER Grant No. DMR-0846426 and partly by Columbia University.
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: Behnaz
full_name: Bozorgui, Behnaz
last_name: Bozorgui
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. The
Journal of Physical Chemistry B. 2010;115(22):7182-7189. doi:10.1021/jp107545w
apa: Šarić, A., Bozorgui, B., & Cacciuto, A. (2010). Packing of soft asymmetric
dumbbells. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/jp107545w
chicago: Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric
Dumbbells.” The Journal of Physical Chemistry B. American Chemical Society,
2010. https://doi.org/10.1021/jp107545w.
ieee: A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,”
The Journal of Physical Chemistry B, vol. 115, no. 22. American Chemical
Society, pp. 7182–7189, 2010.
ista: Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells.
The Journal of Physical Chemistry B. 115(22), 7182–7189.
mla: Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” The Journal
of Physical Chemistry B, vol. 115, no. 22, American Chemical Society, 2010,
pp. 7182–89, doi:10.1021/jp107545w.
short: A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115
(2010) 7182–7189.
date_created: 2021-11-29T15:13:17Z
date_published: 2010-10-15T00:00:00Z
date_updated: 2021-11-29T16:20:29Z
day: '15'
doi: 10.1021/jp107545w
extern: '1'
external_id:
arxiv:
- '1010.2458'
pmid:
- '20949934'
intvolume: ' 115'
issue: '22'
keyword:
- materials chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1010.2458
month: '10'
oa: 1
oa_version: Preprint
page: 7182-7189
pmid: 1
publication: The 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: Packing of soft asymmetric dumbbells
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2010'
...
---
_id: '7780'
abstract:
- lang: eng
text: 'We used single-channel electrical recordings and Langevin molecular dynamics
simulations to explore the electrophoretic translocation of various β-hairpin
peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule
resolution. The β-hairpin peptides, which varied in their folding properties,
corresponded to the C terminal residues of the B1 domain of protein G. The translocation
time was strongly dependent on the electric force and was correlated with the
folding features of the β-hairpin peptides. Highly unfolded peptides entered the
pore in an extended conformation, resulting in fast single-file translocation
events. In contrast, the translocation of the folded β-hairpin peptides occurred
more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a
misfolded or fully folded conformation. This study demonstrates that the interaction
between a polypeptide and a β-barrel protein pore is dependent on the folding
features of the polypeptide. '
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Serdal
full_name: Kirmizialtin, Serdal
last_name: Kirmizialtin
- first_name: Beatrice M.
full_name: Huyghues-Despointes, Beatrice M.
last_name: Huyghues-Despointes
- first_name: Aiping
full_name: Zhu, Aiping
last_name: Zhu
- first_name: J. Martin
full_name: Scholtz, J. Martin
last_name: Scholtz
- first_name: Dmitrii E.
full_name: Makarov, Dmitrii E.
last_name: Makarov
- first_name: Liviu
full_name: Movileanu, Liviu
last_name: Movileanu
citation:
ama: Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, et al. Single-molecule
electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics
simulations. The Journal of Physical Chemistry B. 2007;111(13):3332-3335.
doi:10.1021/jp071364h
apa: Goodrich, C. P., Kirmizialtin, S., Huyghues-Despointes, B. M., Zhu, A., Scholtz,
J. M., Makarov, D. E., & Movileanu, L. (2007). Single-molecule electrophoresis
of β-hairpin peptides by electrical recordings and Langevin dynamics simulations.
The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/jp071364h
chicago: Goodrich, Carl Peter, Serdal Kirmizialtin, Beatrice M. Huyghues-Despointes,
Aiping Zhu, J. Martin Scholtz, Dmitrii E. Makarov, and Liviu Movileanu. “Single-Molecule
Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics
Simulations.” The Journal of Physical Chemistry B. American Chemical Society,
2007. https://doi.org/10.1021/jp071364h.
ieee: C. P. Goodrich et al., “Single-molecule electrophoresis of β-hairpin
peptides by electrical recordings and Langevin dynamics simulations,” The Journal
of Physical Chemistry B, vol. 111, no. 13. American Chemical Society, pp.
3332–3335, 2007.
ista: Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov
DE, Movileanu L. 2007. Single-molecule electrophoresis of β-hairpin peptides by
electrical recordings and Langevin dynamics simulations. The Journal of Physical
Chemistry B. 111(13), 3332–3335.
mla: Goodrich, Carl Peter, et al. “Single-Molecule Electrophoresis of β-Hairpin
Peptides by Electrical Recordings and Langevin Dynamics Simulations.” The Journal
of Physical Chemistry B, vol. 111, no. 13, American Chemical Society, 2007,
pp. 3332–35, doi:10.1021/jp071364h.
short: C.P. Goodrich, S. Kirmizialtin, B.M. Huyghues-Despointes, A. Zhu, J.M. Scholtz,
D.E. Makarov, L. Movileanu, The Journal of Physical Chemistry B 111 (2007) 3332–3335.
date_created: 2020-04-30T12:19:15Z
date_published: 2007-03-13T00:00:00Z
date_updated: 2021-01-12T08:15:29Z
day: '13'
doi: 10.1021/jp071364h
extern: '1'
intvolume: ' 111'
issue: '13'
language:
- iso: eng
month: '03'
oa_version: None
page: 3332-3335
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Single-molecule electrophoresis of β-hairpin peptides by electrical recordings
and Langevin dynamics simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2007'
...
---
_id: '13430'
abstract:
- lang: eng
text: Dynamic self-assembly (DySA) processes occurring outside of thermodynamic
equilibrium underlie many forms of adaptive and intellligent behaviors in natural
systems. Relatively little, however, is known about the principles that govern
DySA and the ways in which it can be extended to artificial ensembles. This article
discusses recent advances in both the theory and the practice of nonequilibrium
self-assembly. It is argued that a union of ideas from thermodynamics and dynamic
systems' theory can provide a general description of DySA. In parallel, heuristic
design rules can be used to construct DySA systems of increasing complexities
based on a variety of suitable interactions/potentials on length scales from nanoscopic
to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Marcin
full_name: Fialkowski, Marcin
last_name: Fialkowski
- first_name: Kyle J. M.
full_name: Bishop, Kyle J. M.
last_name: Bishop
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Stoyan K.
full_name: Smoukov, Stoyan K.
last_name: Smoukov
- first_name: Christopher J.
full_name: Campbell, Christopher J.
last_name: Campbell
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
Principles and implementations of dissipative (dynamic) self-assembly. The
Journal of Physical Chemistry B. 2006;110(6):2482-2496. doi:10.1021/jp054153q
apa: Fialkowski, M., Bishop, K. J. M., Klajn, R., Smoukov, S. K., Campbell, C. J.,
& Grzybowski, B. A. (2006). Principles and implementations of dissipative
(dynamic) self-assembly. The Journal of Physical Chemistry B. American
Chemical Society. https://doi.org/10.1021/jp054153q
chicago: Fialkowski, Marcin, Kyle J. M. Bishop, Rafal Klajn, Stoyan K. Smoukov,
Christopher J. Campbell, and Bartosz A. Grzybowski. “Principles and Implementations
of Dissipative (Dynamic) Self-Assembly.” The Journal of Physical Chemistry
B. American Chemical Society, 2006. https://doi.org/10.1021/jp054153q.
ieee: M. Fialkowski, K. J. M. Bishop, R. Klajn, S. K. Smoukov, C. J. Campbell, and
B. A. Grzybowski, “Principles and implementations of dissipative (dynamic) self-assembly,”
The Journal of Physical Chemistry B, vol. 110, no. 6. American Chemical
Society, pp. 2482–2496, 2006.
ista: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
2006. Principles and implementations of dissipative (dynamic) self-assembly. The
Journal of Physical Chemistry B. 110(6), 2482–2496.
mla: Fialkowski, Marcin, et al. “Principles and Implementations of Dissipative (Dynamic)
Self-Assembly.” The Journal of Physical Chemistry B, vol. 110, no. 6, American
Chemical Society, 2006, pp. 2482–96, doi:10.1021/jp054153q.
short: M. Fialkowski, K.J.M. Bishop, R. Klajn, S.K. Smoukov, C.J. Campbell, B.A.
Grzybowski, The Journal of Physical Chemistry B 110 (2006) 2482–2496.
date_created: 2023-08-01T10:37:35Z
date_published: 2006-01-25T00:00:00Z
date_updated: 2023-08-08T11:33:08Z
day: '25'
doi: 10.1021/jp054153q
extern: '1'
external_id:
pmid:
- '16471845'
intvolume: ' 110'
issue: '6'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '01'
oa_version: None
page: 2482-2496
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Principles and implementations of dissipative (dynamic) self-assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2006'
...