{
  "abstract": "Modeling biomolecular machines with the probability flows on Markov networks often entails computing node probabilities and edge fluxes with master equations and correlating machine performance with entropy production. However, this alone is not sufficient for design, optimization, and evolution because it does not treat cost-benefit trade-offs, topological misflows (backsteps, futile cycles, ineffective actions), or differential properties for flow design. Here, we develop CFT Design, based on the recently developed caliber force theory (CFT). We apply it to designing faster molecular motors through “traffic control”; optimizing speed, energy, and accuracy in kinetic proofreaders simultaneously to break their trade-offs; and designing better enzyme inhibitors based on their network topologies. CFT Design provides a general framework for optimizing nonequilibrium flows.",
  "abstract_shown": true,
  "affiliations": [
    "Stony Brook University"
  ],
  "article_type": "article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Ying-Jen Yang",
      "orcid": "0000-0002-2559-2773"
    },
    {
      "affs": [
        0
      ],
      "name": "Ken A. Dill",
      "orcid": "0000-0002-2390-2002"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5x77d5wepk1vs.bib",
  "cited_by": 0,
  "doi": "10.1103/c8kc-rklj",
  "fulltext_url": null,
  "id": "5x77d5wepk1vs",
  "issns": [
    "2643-1564"
  ],
  "landing_url": "http://link.aps.org/doi/10.1103/c8kc-rklj",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "feed-journal",
      "physics/general"
    ],
    [
      "openalex",
      "3109|Advanced Thermodynamics and Statistical Mechanics"
    ]
  ],
  "openalex": "W7216116716",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-29",
  "publisher": "American Physical Society (APS)",
  "ris": "https://research.draconitic.com/paper/5x77d5wepk1vs.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:18Z",
      "native_id": "10.1103/c8kc-rklj",
      "source": "feed-aps",
      "url": "http://link.aps.org/doi/10.1103/c8kc-rklj"
    },
    {
      "first_seen": "2026-10-30T12:17:55Z",
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      "source": "crossref",
      "url": "https://link.aps.org/doi/10.1103/c8kc-rklj"
    }
  ],
  "subjects": [
    {
      "field": "physics",
      "origin": "openalex:3109|Advanced Thermodynamics and Statistical Mechanics",
      "subfield": "statistical-nonlinear"
    }
  ],
  "title": "Nonequilibrium theory for molecular machine design",
  "title_text": "Nonequilibrium theory for molecular machine design",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:33:17Z",
  "url": "https://research.draconitic.com/paper/5x77d5wepk1vs",
  "venue": "Physical Review Research",
  "versions": [
    {
      "doi": "10.48550/arxiv.2605.09105",
      "pid": "5r1b9knftjfke",
      "relation": "preprint",
      "title": "Nonequilibrium Theory for Molecular Machine Design",
      "venue": "arXiv"
    }
  ]
}