Shortcuts in Stochastic Systems and Control of Biophysical Processes

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

doi:10.1103/physrevx.12.021048

Cited by 17 publications

(7 citation statements)

References 90 publications

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“…[89]. Indeed, a generalization of our framework for general Markov jump processes [43] is related to the stochastic correspondence of shortcuts called shortcuts in stochastic systems [86]. An application of shortcuts or our framework to a low-power electronic circuits called adiabatic circuits [90] is promising.…”

Section: Conclusion and Discussionmentioning

confidence: 99%

“…Finally, we point out that geometric thermodynamics is related to several fascinating topics, and has the potential to clarify the geometric properties of these topics. The classical correspondence of the control protocol called shortcuts to adiabatically for the stochastic process [84][85][86][87][88] is related to the geometry of the probability distribution. Remarkably, the link between shortcuts and information geometry has been proposed in Ref.…”

Section: Conclusion and Discussionmentioning

confidence: 99%

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Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport

Ito

2023

Info. Geo.

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We propose a geometric theory of non-equilibrium thermodynamics, namely geometric thermodynamics, using our recent developments of differential-geometric aspects of entropy production rate in non-equilibrium thermodynamics. By revisiting our recent results on geometrical aspects of entropy production rate in stochastic thermodynamics for the Fokker–Planck equation, we introduce a geometric framework of non-equilibrium thermodynamics in terms of information geometry and optimal transport theory. We show that the proposed geometric framework is useful for obtaining several non-equilibrium thermodynamic relations, such as thermodynamic trade-off relations between the thermodynamic cost and the fluctuation of the observable, optimal protocols for the minimum thermodynamic cost and the decomposition of the entropy production rate for the non-equilibrium system. We clarify several stochastic-thermodynamic links between information geometry and optimal transport theory via the excess entropy production rate based on a relation between the gradient flow expression and information geometry in the space of probability densities and a relation between the velocity field in optimal transport and information geometry in the space of path probability densities.

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Section: Conclusion and Discussionmentioning

confidence: 99%

Section: Conclusion and Discussionmentioning

confidence: 99%

Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport

Ito

2023

Info. Geo.

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“…Evolution control is subject to what is called epistasis, implying some form of interaction (i.e., good or bad in terms of fitness) between two or more mutation (control) variables. This circumstance may favor certain evolutionary pathways but empirically does not necessarily halt the process of an evolving species population at a suboptimal fitness value. ,, Interestingly, recent natural evolution works even drew a parallel with quantum control algorithms. , Additionally, as remarked earlier in Sections and , quantum and classical molecular dynamical control scenarios inherently exploit the coordination among the myriad of control variables to climb their evidently trap-free landscapes. The roles of epistasis remain under debate in natural and directed evolution, including some speculation that high order epistasis among many control variables may smooth out the landscape …”

Section: Natural Evolutionmentioning

confidence: 99%

“…This circumstance may favor certain evolutionary pathways but empirically does not necessarily halt the process of an evolving species population at a suboptimal fitness value. 3,111,120 Interestingly, recent natural evolution works even drew a parallel with quantum control algorithms. 121,122 Additionally, as remarked earlier in Sections 4 and 5, quantum and classical molecular dynamical control scenarios inherently exploit the coordination among the myriad of control variables to climb their evidently trap-free landscapes.…”

Section: Natural Evolutionmentioning

confidence: 99%

The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems

Rabitz

Russell

2023

J. Phys. Chem. A

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This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions�the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources�whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.

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“…The strategy of shortcuts to isothermality has been successfully applied in experiments for a Brownian particle system [75][76][77]. This approach has also been used to construct finite-time heat engines [78][79][80] and control biological evolutions [81,82]. One of the present author and coworkers analyzed the energetics of nonequilibrium processes driven by shortcuts to isothermality [83].…”

mentioning

confidence: 99%

Nonequilibrium work relations meet engineered thermodynamic control: A perspective for nonequilibrium measurements

2023

EPL

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Nonequilibrium work relations establish a fundamental connection between the equilibrium properties of a system and the ﬂuctuation of work performed during nonequilibrium driving processes. However, high dissipation in fast driving processes often impedes the convergence of these work relations, complicating the accurate measurement and estimation of equilibrium properties. To address this issue, recent advances in the methodology of engineered thermodynamic control have been introduced. The goal of this method is to improve the eﬃciency of nonequilibrium measurements by engineering the driving strategies for the system. The engineered strategies enable the system to follow a desired evolution, thereby enhancing the estimation of equilibrium properties in ﬁnite-rate driving processes. In this perspective, we shed light on recent developments in this ﬁeld. Diﬀerent principles have been reviewed for engineering thermodynamic driving strategies, such as ﬁnding optimal control protocols to minimize dissipation and designing thermodynamic control protocols to shorten the lag between the system current state and its corresponding equilibrium state. Nonequilibrium measurement schemes matched with engineered thermodynamic control are also outlined as promising avenues for improving the eﬃciency and accuracy of nonequilibrium measurements, including several reﬁned nonequilibrium work relations matched with designed thermodynamic control protocols.

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Shortcuts in Stochastic Systems and Control of Biophysical Processes

Cited by 17 publications

References 90 publications

Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport

Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport

The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems

Nonequilibrium work relations meet engineered thermodynamic control: A perspective for nonequilibrium measurements

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