{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Fachbereich Chemie, Philipps-Universität Marburg, 35032Marburg, Germany.",
    "Department of Chemistry, University of California, Irvine, Irvine, California92697, United States."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Rinto Thomas",
      "orcid": "0000-0003-3781-8503"
    },
    {
      "affs": [
        1
      ],
      "name": "Praveen Ranganath Prabhakar",
      "orcid": "0000-0002-7924-0693"
    },
    {
      "affs": [
        0
      ],
      "name": "Michael von Domaros",
      "orcid": "0000-0003-0111-4141"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7t700a2v49f69.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jctc.6c00645",
  "fulltext_url": "https://europepmc.org/articles/PMC13602916",
  "id": "7t700a2v49f69",
  "issns": [
    "1549-9618",
    "1549-9626"
  ],
  "landing_url": "https://europepmc.org/article/MED/42917446",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1606|Advanced Physical and Chemical Molecular Interactions"
    ]
  ],
  "openalex": "W7148911044",
  "pdf_url": "https://europepmc.org/articles/PMC13602916?pdf=render",
  "pmcid": "PMC13602916",
  "pmid": "42917446",
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7t700a2v49f69.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:02Z",
      "native_id": "MED:42917446",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42917446"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1606|Advanced Physical and Chemical Molecular Interactions",
      "subfield": "physical"
    }
  ],
  "title": "A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations.",
  "title_text": "A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:21:02Z",
  "url": "https://research.draconitic.com/paper/7t700a2v49f69",
  "venue": "Journal of chemical theory and computation",
  "versions": []
}