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

TL;DR

This paper analytically explores how biological networks balance energy, speed, and accuracy in substrate discrimination, revealing conditions under which these trade-offs are asymptotically finite or infinite, with implications for cellular processes.

Contribution

It introduces a linear framework and a parameter scaling method to analyze complex networks' energy-speed-accuracy relations beyond simple or equilibrium assumptions.

Findings

Identifies classes of networks where the energy-speed-accuracy ratio remains finite as accuracy improves.

Shows that even simple networks like Hopfield's can exhibit parametric complexity with infinite ratios.

Suggests bounds on the ratio under certain parametric assumptions, relevant for biological discrimination mechanisms.

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.