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Open Access Publications from the University of California

Scholarly Works (3 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2023)
We develop a theory for inferring equilibrium transition rates from trajectories driven by a time-dependent force using results from stochastic thermodynamics. Applying the Kawasaki relation to approximate the nonequilibrium distribution function in terms of the equilibrium distribution function and the excess dissipation, we formulate a nonequilibrium transition state theory to estimate the rate enhancement over the equilibrium rate due to the nonequilibrium protocol. We demonstrate the utility of our theory in examples of pulling of harmonically trapped particles in one and two dimensions, as well as a semiflexible polymer with a reactive linker in three dimensions. We expect our purely thermodynamic approach will find use in both molecular simulation and force spectroscopy experiments.
    Cover page: Inferring equilibrium transition rates from nonequilibrium protocols.
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2021)
    Complex systems can convert energy imparted by nonequilibrium forces to regulate how quickly they transition between long-lived states. While such behavior is ubiquitous in natural and synthetic systems, currently there is no general framework to relate the enhancement of a transition rate to the energy dissipated or to bound the enhancement achievable for a given energy expenditure. We employ recent advances in stochastic thermodynamics to build such a framework, which can be used to gain mechanistic insight into transitions far from equilibrium. We show that under general conditions, there is a basic speed limit relating the typical excess heat dissipated throughout a transition and the rate amplification achievable. We illustrate this tradeoff in canonical examples of diffusive barrier crossings in systems driven with autonomous and deterministic external forcing protocols. In both cases, we find that our speed limit tightly constrains the rate enhancement.
      Cover page: Dissipation bounds the amplification of transition rates far from equilibrium
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2023)

      Rare events are ubiquitous in noisy complex systems throughout the physical sciences and to large extent determine their function and regulation. Dissipative outside forces often work hand in hand with equilibrium structure to shape the mechanism and frequency of such improbable fluctuations, but little is known about how to codify the influence of non-equilibrium on reaction rates and their mechanisms. In the last quarter century we have seen paradigm shifting breakthroughs in reaction rate theory that have allowed for the study of rare transitions in complex many particle systems. At the same time, development of the statistical mechanics of trajectories has revolutionized how we study the behavior, response and functional limits of systems away from equilibrium. Here, we develop a trajectory theory of how reaction rates respond to nonequilibrium forces, allowing us both to probe how non-equilibrium systems regulate their function, and leverage optimally designed forces to sample reaction rates from finite time driven trajectories for the first time.

        Cover page: Mountains and rivers: rare events in noisy systems and the forces that shape them
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