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| Main Authors: | , , |
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| Format: | Preprint |
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2026
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2604.01940 |
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| _version_ | 1866911562971742208 |
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| author | Thomas, Rinto Prabhakar, Praveen Ranganath von Domaros, Michael |
| author_facet | Thomas, Rinto Prabhakar, Praveen Ranganath von Domaros, Michael |
| contents | We introduce a residence-time approach (RTA) for determining position-dependent diffusivities from biased molecular dynamics simulations. The method is formulated for trajectory segments in which the effective drift along the transport coordinate is negligible, as realized here using adaptive biasing force simulations. In this regime, local diffusivities are obtained directly from mean first-exit times out of finite spatial intervals. Unlike conventional fluctuation-based approaches, the RTA does not require dedicated harmonically restrained simulations or numerical integration of noisy time-correlation functions. We assess the method for oxygen diffusion across a hexadecane slab, water permeation across a lipid bilayer, and permeation of water and selected volatile organic compounds through a model skin-barrier membrane. In the slab system, the RTA reproduces independently determined bulk diffusivities within statistical uncertainty. In the membrane systems, the inferred diffusivity profiles are supported by propagator-level validation. These results establish the RTA as a practical approach for extracting position-dependent diffusivities from biased molecular simulations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2604_01940 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations Thomas, Rinto Prabhakar, Praveen Ranganath von Domaros, Michael Soft Condensed Matter Biological Physics Chemical Physics We introduce a residence-time approach (RTA) for determining position-dependent diffusivities from biased molecular dynamics simulations. The method is formulated for trajectory segments in which the effective drift along the transport coordinate is negligible, as realized here using adaptive biasing force simulations. In this regime, local diffusivities are obtained directly from mean first-exit times out of finite spatial intervals. Unlike conventional fluctuation-based approaches, the RTA does not require dedicated harmonically restrained simulations or numerical integration of noisy time-correlation functions. We assess the method for oxygen diffusion across a hexadecane slab, water permeation across a lipid bilayer, and permeation of water and selected volatile organic compounds through a model skin-barrier membrane. In the slab system, the RTA reproduces independently determined bulk diffusivities within statistical uncertainty. In the membrane systems, the inferred diffusivity profiles are supported by propagator-level validation. These results establish the RTA as a practical approach for extracting position-dependent diffusivities from biased molecular simulations. |
| title | A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations |
| topic | Soft Condensed Matter Biological Physics Chemical Physics |
| url | https://arxiv.org/abs/2604.01940 |