A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions
Hosseini, Atiyeh Najla ; Lund, Mikael LU
and Ejtehadi, Mohammad Reza
(2022)
In Physical Chemistry Chemical Physics
24(6).
p.3647-3654
- Abstract
Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of pulling forces in backward and forward... (More)
Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of pulling forces in backward and forward directions for the Jarzynski free-energy estimator using steered molecular dynamics simulation. Our results show that this leads to much improvement for NP-membrane translocation free energies. Although here we have demonstrated the application of the method in molecular dynamics simulation, it could be applied for experimental approaches.
(Less)
- author
- Hosseini, Atiyeh Najla
; Lund, Mikael
LU
and Ejtehadi, Mohammad Reza
- organization
- publishing date
- 2022-02-14
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Physical Chemistry Chemical Physics
- volume
- 24
- issue
- 6
- pages
- 8 pages
- publisher
- Royal Society of Chemistry
- external identifiers
-
- pmid:35103740
- scopus:85124443728
- ISSN
- 1463-9076
- DOI
- 10.1039/d1cp05218g
- language
- English
- LU publication?
- yes
- additional info
- Publisher Copyright: © 2022 the Owner Societies.
- id
- cf0fab58-5ad7-44bb-9ea6-a4862e5e1aff
- date added to LUP
- 2022-02-28 17:49:36
- date last changed
- 2025-02-16 18:18:20
@article{cf0fab58-5ad7-44bb-9ea6-a4862e5e1aff,
abstract = {{<p>Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of pulling forces in backward and forward directions for the Jarzynski free-energy estimator using steered molecular dynamics simulation. Our results show that this leads to much improvement for NP-membrane translocation free energies. Although here we have demonstrated the application of the method in molecular dynamics simulation, it could be applied for experimental approaches. </p>}},
author = {{Hosseini, Atiyeh Najla and Lund, Mikael and Ejtehadi, Mohammad Reza}},
issn = {{1463-9076}},
language = {{eng}},
month = {{02}},
number = {{6}},
pages = {{3647--3654}},
publisher = {{Royal Society of Chemistry}},
series = {{Physical Chemistry Chemical Physics}},
title = {{A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions}},
url = {{http://dx.doi.org/10.1039/d1cp05218g}},
doi = {{10.1039/d1cp05218g}},
volume = {{24}},
year = {{2022}},
}