Nonequilibrium Response for Markov Jump Processes: Exact Results and Tight Bounds

Physical Review Letters, Journal Year: 2024, Volume and Issue: 132(3)

Published: Jan. 16, 2024

Generalizing response theory of open systems far from equilibrium is a central quest nonequilibrium statistical physics. Using stochastic thermodynamics, we develop an algebraic method to study the static steady state arbitrary perturbations. This allows us derive explicit expressions for edge currents as well traffic perturbations in kinetic barriers and driving forces. We also show that these responses satisfy very simple bounds. For energy perturbations, straightforwardly recover results obtained using nontrivial graph-theoretical methods.Received 16 August 2023Revised 13 October 2023Accepted 14 December 2023DOI:https://doi.org/10.1103/PhysRevLett.132.037101© 2024 American Physical SocietyPhysics Subject Headings (PhySH)Research AreasNonequilibrium mechanicsStochastic thermodynamicsTechniquesLinear theoryStatistical Physics & Thermodynamics

Language: Английский

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Dynamical activity universally bounds precision of response in Markovian nonequilibrium systems

Communications Physics, Journal Year: 2025, Volume and Issue: 8(1)

Published: Feb. 11, 2025

Language: Английский

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Input-to-State Stabilization for Markov Jump Systems With Dynamic Quantization and Multimode Injection Attacks

IEEE Transactions on Systems Man and Cybernetics Systems, Journal Year: 2024, Volume and Issue: 54(4), P. 2517 - 2529

Published: Jan. 12, 2024

This article explores observer-based input-to-state stabilization for Markov jump systems with both dynamic input and output quantization, as well multimode injection attacks (IAs). The chain of the plant, together IAs described by two stochastic processes following categorical distribution, constitutes a pair hidden models. A sufficient condition mean-square stability feedback control system is proposed utilizing Lyapunov-type function dependent on mode exponential decay rate, S-procedure, several analysis tools. Then, two-stage approach, which required controller observer gains scaling factors can be determined successively, developed. are constructed piecewise functions, excluding possibility singularities involved in previous quantized approaches. Under zero initial condition, greedy backtracking suboptimization algorithm further put forward, offering an estimate minimum permissible upper bound closed-loop state bounded disturbance input, given fixed rate. Finally, vertical lift aircraft model applied to validate approach algorithm.

Language: Английский

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Thermodynamic Bounds on Symmetry Breaking in Linear and Catalytic Biochemical Systems

Physical Review Letters, Journal Year: 2024, Volume and Issue: 132(22)

Published: May 31, 2024

Living systems are maintained out of equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break symmetries and originate from the expansion accessible chemical space due to nonequilibrium conditions. Here, we use matrix-tree theorem derive upper lower thermodynamic bounds on these symmetry-breaking features in linear catalytic biochemical systems. Our independent kinetics hold for both closed open reaction networks. We also extend our results master equations space. Using framework, recover constraints kinetic proofreading. Finally, show contrast reaction-diffusion patterns can be bounded only force. provide a general framework understanding role conditions shaping steady-state properties Published American Physical Society 2024

Language: Английский

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A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

eLife, Journal Year: 2025, Volume and Issue: 14

Published: March 17, 2025

The Gillespie algorithm is commonly used to simulate and analyze complex chemical reaction networks. Here, we leverage recent breakthroughs in deep learning develop a fully differentiable variant of the algorithm. (DGA) approximates discontinuous operations exact using smooth functions, allowing for calculation gradients backpropagation. DGA can be quickly accurately learn kinetic parameters gradient descent design biochemical networks with desired properties. As an illustration, apply study stochastic models gene promoters. We show that to: (1) successfully from experimental measurements mRNA expression levels two distinct Escherichia coli promoters (2) nonequilibrium promoter architectures input–output relationships. These examples illustrate utility analyzing kinetics, including wide variety problems interest synthetic systems biology.

Language: Английский

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Structural constraints limit the regime of optimal flux in autocatalytic reaction networks

Communications Physics, Journal Year: 2024, Volume and Issue: 7(1)

Published: July 9, 2024

Abstract Autocatalytic chemical networks play a predominant role in large number of natural systems such as metabolic pathways and ecological networks. Despite recent efforts, the precise impact thermodynamic constraints on these remains elusive. In this work, we present theoretical framework that allows specific bounds affinity concentrations autocatalysts mass-action autocatalytic These can be obtained solely from stoichiometry underlying reaction network, are independent numerical values kinetic parameters. This property holds regime where all fluxes network tightly coupled maximal. Our method is applicable to networks, used complement constraints-based modeling methods which typically do not provide predictions about properties or concentration ranges metabolites.

Language: Английский

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General Theory of Static Response for Markov Jump Processes

Physical Review Letters, Journal Year: 2024, Volume and Issue: 133(10)

Published: Sept. 5, 2024

We consider Markov jump processes on a graph described by rate matrix that depends various control parameters. derive explicit expressions for the static responses of edge currents and steady-state probabilities. show they are constrained topology (i.e., incidence matrix) deriving response relations linear constraints linking different responses) topology-dependent bounds. For unicyclic networks, all scaled current between zero one must sum to one. Applying these results stochastic thermodynamics, we fundamental (which carry full dissipation) thermodynamic forces drive system away from equilibrium).

Language: Английский

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Flexibility and sensitivity in gene regulation out of equilibrium

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(46)

Published: Nov. 5, 2024

Cells adapt to environments and tune gene expression by controlling the concentrations of proteins their kinetics in regulatory networks. In both eukaryotes prokaryotes, experiments theory increasingly attest that these networks can do consume biochemical energy. How does this dissipation enable cellular behaviors forbidden equilibrium? This open question demands quantitative models transcend thermodynamic equilibrium. Here, we study control simple, ubiquitous explore consequences departing equilibrium transcription. Employing graph model a set especially common motifs, find unlocks nonmonotonicity enhanced sensitivity with respect transcription factor’s concentration. These features allow single factor act as repressor activator at different or achieve outputs multiple concentration regimes locally sensitivity. We systematically dissect how energetically driving individual transitions within networks, pairs transitions, generates wide range more adjustable sensitive phenotypic responses than results generalize complex scenarios, including combinatorial factors, which relate often collapse simple mathematical behaviors. Our findings quantify necessary conditions detectable energy expenditure. richer behaviors—feasibly accessed using biological budgets rates—may empower cells accomplish sophisticated regulation simpler architectures those required

Language: Английский

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Flexibility and sensitivity in gene regulation out of equilibrium

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 13, 2023

Cells adapt to environments and tune gene expression by controlling the concentrations of proteins their kinetics in regulatory networks. In both eukaryotes prokaryotes, experiments theory increasingly attest that these networks can do consume bio-chemical energy. How does this dissipation enable cellular behaviors unobtainable equilibrium? This open question demands quantitative models transcend thermodynamic equilibrium. Here we study control a simple, ubiquitous motif explore consequences departing equilibrium kinetic cycles. Employing graph theory, find unlocks nonmonotonicity enhanced sensitivity with respect transcription factor's concentration. These features allow single factor act as repressor activator at different levels or achieve outputs multiple concentration regions locally-enhanced sensitivity. We systematically dissect how energetically-driving individual transitions within networks, pairs transitions, generates more adjustable sensitive phenotypic responses. Our findings quantify necessary conditions detectable energy expenditure. richer mathematical behaviors-feasibly accessed using biological budgets rates-may empower cells accomplish sophisticated regulation simpler architectures than those required

Language: Английский

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Topologically constrained fluctuations and thermodynamics regulate nonequilibrium response

Physical review. E, Journal Year: 2023, Volume and Issue: 108(4)

Published: Oct. 6, 2023

Near equilibrium, the fluctuation-dissipation theorem is an important tool in understanding how a system responds to external perturbations. Here authors derive expressions that describe response of physical observables outside terms both topology microscopic state space and strength thermodynamic driving.

Language: Английский

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