期刊
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
卷 24, 期 6, 页码 3647-3654出版社
ROYAL SOC CHEMISTRY
DOI: 10.1039/d1cp05218g
关键词
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资金
- Foundation of the Royal Swedish Academy of Sciences
- Ministry of Science, Research, and Technology of Iran
This article introduces a correction Pair Forces method to improve the accuracy of NP-membrane translocation free energy calculations by calculating the forward and backward pulling forces for the Jarzynski free-energy estimator using steered molecular dynamics simulation.
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.
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