Shortcuts in Stochastic Systems and Control of Biophysical Processes

Ilker, Efe; Güngör, Özenç; Kuznets-Speck, Benjamin; Chiel, Joshua; Deffner, Sebastian; Hinczewski, Michael

doi:10.1103/PhysRevX.12.021048

Title: Shortcuts in Stochastic Systems and Control of Biophysical Processes

Journal Article · Tue May 31 00:00:00 EDT 2022 · Physical Review. X

DOI:https://doi.org/10.1103/PhysRevX.12.021048· OSTI ID:1870540

; Güngör, Özenç;

;

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 nonstationary targets and local control—where only a subset of system states is 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.

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Research Organization:: Case Western Reserve Univ., Cleveland, OH (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); LabEx Cell(n)Scale

Grant/Contract Number:: DOE-SC0009946; SC0009946; MCB-1651650; ANR-11-LABX-0038; ANR-10-IDEX-0001-02; DGE 1840340

OSTI ID:: 1870540

Alternate ID(s):: OSTI ID: 1980367

Journal Information:: Physical Review. X, Journal Name: Physical Review. X Vol. 12 Journal Issue: 2; ISSN 2160-3308

Publisher:: American Physical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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