A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations.
- 1Fachbereich Chemie, Philipps-Universität Marburg, 35032Marburg, Germany.
- 2Department of Chemistry, University of California, Irvine, Irvine, California92697, United States.
Abstract
Position-dependent diffusivities are central parameters in reduced stochastic descriptions of molecular transport in heterogeneous environments, but their reliable estimation from molecular dynamics simulations remains challenging. We present a residence-time approach (RTA) that extracts local diffusivities from first-exit statistics measured in biased simulations after compensation of the mean free-energy gradient. We apply the method to oxygen diffusion across a hexadecane/water slab, water permeation across a POPC lipid bilayer, and transport of water and volatile organic compounds through a model skin-barrier membrane. In the slab system, RTA diffusivities agree with independently determined bulk reference values. In the membrane systems, propagator predictions based on RTA-derived diffusivities reproduce unbiased molecular dynamics propagators over substantial lag-time ranges, while also revealing that, in some cases, no single lag-time-independent diffusivity profile captures the dynamics across all time scales. These results support residence-time statistics as a practical route for determining effective position-dependent diffusivities from biased molecular simulations.
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BibTeX
@article{thomas2026residencetime,
title = {{A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations.}},
author = {Rinto Thomas and Praveen Ranganath Prabhakar and Michael von Domaros},
journal = {Journal of chemical theory and computation},
year = {2026},
month = sep,
doi = {10.1021/acs.jctc.6c00645},
url = {https://europepmc.org/article/MED/42917446},
note = {CC BY},
}
RIS
TY - JOUR
TI - A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations.
AU - Rinto Thomas
AU - Praveen Ranganath Prabhakar
AU - Michael von Domaros
PY - 2026
DA - 2026/09/01
JO - Journal of chemical theory and computation
DO - 10.1021/acs.jctc.6c00645
UR - https://europepmc.org/article/MED/42917446
AB - Position-dependent diffusivities are central parameters in reduced stochastic descriptions of molecular transport in heterogeneous environments, but their reliable estimation from molecular dynamics simulations remains challenging. We present a residence-time approach (RTA) that extracts local diffusivities from first-exit statistics measured in biased simulations after compensation of the mean free-energy gradient. We apply the method to oxygen diffusion across a hexadecane/water slab, water permeation across a POPC lipid bilayer, and transport of water and volatile organic compounds through a model skin-barrier membrane. In the slab system, RTA diffusivities agree with independently determined bulk reference values. In the membrane systems, propagator predictions based on RTA-derived diffusivities reproduce unbiased molecular dynamics propagators over substantial lag-time ranges, while also revealing that, in some cases, no single lag-time-independent diffusivity profile captures the dynamics across all time scales. These results support residence-time statistics as a practical route for determining effective position-dependent diffusivities from biased molecular simulations.
SN - 1549-9618
SN - 1549-9626
ER -