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

Atiyeh Najla Hosseini, Mikael Lund, Mohammad Reza Ejtehadi

Research output: Contribution to journalArticlepeer-review

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 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.

Original languageEnglish
Pages (from-to)3647-3654
Number of pages8
JournalPhysical Chemistry Chemical Physics
Volume24
Issue number6
DOIs
Publication statusPublished - 2022 Feb 14

Subject classification (UKÄ)

  • Theoretical Chemistry
  • Biophysics

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