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

Summary, in English

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.

• Author: Atiyeh Najla Hosseini; Mikael Lund; Mohammad Reza Ejtehadi
• Department/s: Computational Chemistry; eSSENCE: The e-Science Collaboration; LINXS - Institute of advanced Neutron and X-ray Science
• Publishing year: 2022-02-14
• Language: English
• Pages: 3647-3654
• Publication/Series: Physical Chemistry Chemical Physics
• Volume: 24
• Issue: 6
• Links: http://dx.doi.org/10.1039/d1cp05218g
• Document type: Journal article
• Publisher: Royal Society of Chemistry
• Topic: Theoretical Chemistry (including Computational Chemistry); Biophysics
• Status: Published
• ISBN/ISSN/Other: ISSN: 1463-9076