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Peer-reviewedCC BY 4.0Physical Review Research

Nonequilibrium theory for molecular machine design

  • Ying-Jen Yang1
  • Ken A. Dill1
  1. 1Stony Brook University
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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.

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Cite

BibTeXRIS
BibTeX
@article{yang2026nonequilibrium,
  title = {{Nonequilibrium theory for molecular machine design}},
  author = {Ying-Jen Yang and Ken A. Dill},
  journal = {Physical Review Research},
  year = {2026},
  month = oct,
  doi = {10.1103/c8kc-rklj},
  url = {http://link.aps.org/doi/10.1103/c8kc-rklj},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Nonequilibrium theory for molecular machine design
AU  - Ying-Jen Yang
AU  - Ken A. Dill
PY  - 2026
DA  - 2026/10/29
JO  - Physical Review Research
DO  - 10.1103/c8kc-rklj
UR  - http://link.aps.org/doi/10.1103/c8kc-rklj
AB  - 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.
SN  - 2643-1564
ER  -