Dissipation in noisy chemical networks: The role of deficiency

Abstract

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, only when deficiency is zero does the average stochastic dissipation rate equal that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers.

10 Pages, 6 figures

References in corpus (9)

• Ensemble and Trajectory Thermodynamics: A Brief Introduction
• Stochastic thermodynamics of chemical reaction networks
• Stochastic fluctuations in metabolic pathways
• Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws
• Amplified biochemical oscillations in cellular systems
• Product-form Poisson-like distributions and complex balanced reaction systems
• Validity conditions for moment closure approximations in stochastic chemical kinetics
• Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs
• Transient fluctuation theorems for the currents and initial equilibrium ensembles

Cited by in corpus (23)

• Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics
• Effective thermodynamics for a marginal observer
• Conservation Laws and Work Fluctuation Relations in Chemical Reaction Networks
• Fluctuation-dissipation relations far from equilibrium
• Large deviations and dynamical phase transitions in stochastic chemical networks
• Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten
• Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law
• Nonequilibrium Thermodynamic Formalism of Nonlinear Chemical Reaction Systems with Waage-Guldberg's Law of Mass Action
• Conservation laws and symmetries in stochastic thermodynamics
• Milestoning estimators of dissipation in systems observed at a coarse resolution: When ignorance is truly bliss
• Stochastic thermodynamics of all-to-all interacting many-body systems
• Methods and Conversations in (Post)Modern Thermodynamics
• Bond Graph Representation of Chemical Reaction Networks
• Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization
• Trade-offs between number fluctuations and response in nonequilibrium chemical reaction networks
• Broken detailed balance and entropy production in directed networks
• Stochastic approach to entropy production in chemical chaos
• Solving Moment Hierarchies for Chemical Reaction Networks
• Optimal inference strategies and their implications for the linear noise approximation
• On non-ideal chemical-reaction networks and phase separation
• Deficiency, Kinetic Invertibility, and Catalysis in Stochastic Chemical Reaction Networks
• Eikonal solutions for moment hierarchies of Chemical Reaction Networks in the limits of large particle number
• Insights into the relation between noise and biological complexity