Modeling of biomolecular machines in non-equilibrium steady states

  title={Modeling of biomolecular machines in non-equilibrium steady states},
  author={Thomas Speck},
  journal={The Journal of Chemical Physics},
  • T. Speck
  • Published 8 September 2021
  • Physics
  • The Journal of Chemical Physics
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling–even if often this step is not made explicit–and any model has to neglect details while still being physically accurate. Equilibrium statistical mechanics guides both the development of models and numerical methods for dynamics obeying detailed balance. For systems driven away from thermal equilibrium such a universal theoretical framework is missing. For a restricted class of… 

Figures and Tables from this paper

Survival and extreme statistics of work, heat, and entropy production in steady-state heat engines
Gonzalo Manzano 2 and Édgar Roldán Institute for Cross-Disciplinary Physics and Complex Systems IFISC (UIB-CSIC), Campus Universitat Illes Balears, E-07122 Palma de Mallorca, Spain. Institute for


Non-equilibrium Markov state modeling of periodically driven biomolecules.
This work introduces a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter, and illustrates the method for alanine dipeptide exposed to a time-dependent electric field.
Markov state models of biomolecular conformational dynamics.
  • J. Chodera, F. Noé
  • Computer Science, Medicine
    Current opinion in structural biology
  • 2014
Stochastic thermodynamics of single enzymes and molecular motors
  • U. Seifert
  • Physics, Biology
    The European physical journal. E, Soft matter
  • 2011
The present approach highlights both the crucial role of the intrinsic entropy of each state and the physically questionable role of chemiostats for deriving the first law for molecular motors subject to an external force under realistic conditions.
Stochastic thermodynamics, fluctuation theorems and molecular machines.
  • U. Seifert
  • Physics, Biology
    Reports on progress in physics. Physical Society
  • 2012
Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.
Markov models of molecular kinetics: generation and validation.
An upper bound for the approximation error made by modeling molecular dynamics with a Markov chain is described and it is shown that this error can be made arbitrarily small with surprisingly little effort.
Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information.
This work proposes a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables and employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales.
From Stochastic Thermodynamics to Thermodynamic Inference
  • U. Seifert
  • Physics
    Annual Review of Condensed Matter Physics
  • 2019
For a large class of nonequilibrium systems, thermodynamic notions like work, heat, and, in particular, entropy production can be identified on the level of fluctuating dynamical trajectories. Within
Coarse graining of biochemical systems described by discrete stochastic dynamics.
A criterion for the optimal level of coarse graining or resolution of the process is proposed via a tradeoff between the simplicity of the coarse-grained model and the information loss relative to the original model.
Fluctuation theorems and the nonequilibrium thermodynamics of molecular motors.
  • D. Andrieux, P. Gaspard
  • Physics, Medicine
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2006
It is shown that the fluctuation theorems provide a method to determine the affinity or thermodynamic force driving the motor, given in terms of the free enthalpy of the chemical reactions.