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A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions

Hosseini, A. N ; Sharif University of Technology | 2022

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  1. Type of Document: Article
  2. DOI: 10.1039/d1cp05218g
  3. Publisher: Royal Society of Chemistry , 2022
  4. Abstract:
  5. 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. © 2022 the Owner Societies
  6. Keywords:
  7. Molecular dynamics ; Nanoparticles ; Biomolecular process ; Coated nanoparticles ; Force application ; ITS applications ; Membrane interactions ; Nanoparticle membranes ; Nanoparticle uptakes ; Nanoscale levels ; Non-conservative forces ; Time-scales ; Free energy ; Nanoparticle ; Entropy ; Molecular dynamics ; Thermodynamics ; Entropy ; Molecular Dynamics Simulation ; Nanoparticles ; Thermodynamics
  8. Source: Physical Chemistry Chemical Physics ; Volume 24, Issue 6 , 2022 , Pages 3647-3654 ; 14639076 (ISSN)
  9. URL: https://pubs.rsc.org/en/content/articlelanding/2022/cp/d1cp05218g