Shortcuts in Stochastic Systems and Control of Biophysical Processes
Shortcuts in Stochastic Systems and Control of Biophysical Processes
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随机系统和生物物理过程控制的捷径
DOI：
10.1103/physrevx.12.021048
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发表时间：
2022
影响因子：
12.5
通讯作者：
Hinczewski, Michael
中科院分区：
文献类型：
--
作者：
Ilker, Efe;Güngör, Özenç;Kuznets-Speck, Benjamin;Chiel, Joshua;Deffner, Sebastian;Hinczewski, Michael
调节生命系统的生化反应网络都具有不同程度的随机性。由此产生的随机性在多个尺度上影响生物学结果，从细胞中单个蛋白质的功能状态到整个种群的进化轨迹。控制这些结果的分布如何随时间变化——通过外部干预，如随时间变化的化学物质浓度——是一项复杂的挑战。在这项工作中，我们展示了最初用于控制量子系统的反绝热（CD）驱动如何为指导生物过程提供了一种通用工具。我们开发了一个实用的图论框架，用于离散状态连续马尔可夫网络中的CD驱动。尽管CD驱动仅限于具有瞬时稳态的目标轨迹，但我们展示了如何推广该方法以允许非稳态目标和局部控制-其中仅针对系统状态的子集。后者对于可能只有少量可用的外部控制旋钮，不足以进行全局控制的生物实现特别有用。我们推导出简单的图形标准，说明何时可以进行局部控制或全局控制。最后，我们说明了在伴侣辅助蛋白折叠中遗传调控开关的全局控制和局部控制的形式主义。在伴侣系统中导出的控制方案与酵母和e热休克反应的实验测量中看到的自然控制策略非常相似。杆菌。
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 andE. coli.