Nonequilibrium Theory for Molecular Machine Design
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient for design, optimization and evolution because it doesn't treat cost-benefit tradeoffs, or small-system 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; and designing better enzyme inhibitors. CFT Design provides a general framework for optimizing nonequilibrium flow networks.