An energy-speed-accuracy relation in complex networks for biological discrimination

Abstract

Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous studies have focussed on biochemical networks with simple structure or relied on simplifying kinetic assumptions. Here, we use the linear framework for timescale separation to analytically examine steady-state probabilities away from thermodynamic equilibrium for networks of arbitrary complexity. We also introduce a method of scaling parameters that is inspired by Hopfield's treatment of kinetic proofreading. Scaling allows asymptotic exploration of high-dimensional parameter spaces. We identify in this way a broad class of complex networks and scalings for which the quantity $\sigma \ln (\mu )/P$ remains asymptotically finite whenever accuracy improves from equilibrium, so that ${\mu }_{eq}/\mu \to 0$. Scalings exist, however, even for Hopfield's original network, for which $\sigma \ln (\mu )/P$ is asymptotically infinite, illustrating the parametric complexity. Outside the asymptotic regime, numerical calculations suggest that, under more restrictive parametric assumptions, networks satisfy the bound, $\sigma \ln (\mu /{\mu }_{eq})/P<1$, and we discuss the biological implications for discrimination by ribosomes and DNA polymerase. The methods introduced here may be more broadly useful for analysing complex networks that implement other forms of cellular information processing.

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Cited by in corpus (12)

• Universal thermodynamic bounds on nonequilibrium response with biochemical applications
• Kinetic Proofreading and the Limits of Thermodynamic Uncertainty
• The energy cost and optimal design of networks for biological discrimination
• Thermodynamic uncertainty relation to assess biological processes
• Topologically-constrained fluctuations and thermodynamics regulate nonequilibrium response
• Reversal symmetries for cyclic paths away from thermodynamic equilibrium
• Allostery and Kinetic Proofreading
• Pareto optimal fronts of kinetic proofreading
• Noise induced new quasi-period and periods switching
• Processive and Distributive Non-Equilibrium Networks Discriminate in Alternate Limits
• Interplay of energy, dissipation, and error in kinetic proofreading: Control via concentration and binding energy
• Reformulating non-equilibrium steady-states and generalised Hopfield discrimination