Shortcuts in stochastic systems and control of biophysical processes

Abstract

The biochemical reaction networks that regulate living systems are all stochastic to varying degrees. The resulting randomness affects biological outcomes at multiple scales, from the functional states of single proteins in a cell to the evolutionary trajectory of whole populations. Controlling how the distribution of these outcomes changes over time -- via external interventions like time-varying concentrations of chemical species -- is a complex challenge. In this work, we show how counterdiabatic (CD) driving, first developed to control quantum systems, provides a versatile tool for steering biological processes. We develop a practical graph-theoretic framework for CD driving in discrete-state continuous-time Markov networks. Though CD driving is limited to target trajectories that are instantaneous stationary states, we show how to generalize the approach to allow for non-stationary targets and local control -- where only a subset of system states are targeted. The latter is particularly useful for biological implementations where there may be only a small number of available external control knobs, insufficient for global control. We derive simple graphical criteria for when local versus global control is possible. Finally, we illustrate the formalism with global control of a genetic regulatory switch and local control in chaperone-assisted protein folding. The derived control protocols in the chaperone system closely resemble natural control strategies seen in experimental measurements of heat shock response in yeast and E. coli.

main text: 27 pages, 9 figures; revision includes extension of theory to cover non-stationary targets and local control, with updated biological examples

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Cited by in corpus (13)

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• Limited-control optimal protocols arbitrarily far from equilibrium
• Optimizing Brownian heat engine with shortcut strategy
• Shortcuts to thermodynamic quasistaticity
• Mutual Multilinearity of Nonequilibrium Network Currents
• Geometric thermodynamics of reaction-diffusion systems: Thermodynamic trade-off relations and optimal transport for pattern formation
• Infinite variety of thermodynamic speed limits with general activities
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• Time-Asymmetric Fluctuation Theorem and Efficient Free Energy Estimation
• Riemannian Geometry of Optimal Driving and Thermodynamic Length and its Application to Chemical Reaction Networks