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Nonequilibrium Theory for Molecular Machine Design
Ying-Jen Yang, Ken A. Dill
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance…
Fluctuation-Response Design Rules for Nonequilibrium Flows
Ying-Jen Yang, Ken A. Dill
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on f…
Nonequilibrium Theory for Adaptive Systems in Varying Environments
Ying-Jen Yang, Charles D. Kocher, Ken A. Dill
Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two co…
A Principled Basis for Nonequilibrium Network Flows
Ying-Jen Yang, Ken A. Dill
The great power of EQuilibrium (EQ) statistical physics comes from its principled foundations: its First Law (conservation), Second Law (variational tendency principle), and its Le…
Deriving the Forces of Nonequilibria from Two Laws
Ying-Jen Yang, Ken A. Dill
Non-EQuilibrium (NEQ) statistical physics has not had the same general foundation as that of EQuilibrium (EQ) statistical physics, where forces are derived from potentials such as…