Pareto optimal fronts of kinetic proofreading

Abstract: Biological processes such as DNA replication, RNA transcription, and protein translation show remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by nonequilibrium reactions that dissipate chemical energy. It is widely recognized that there must be a trade-off between speed, error, and dissipation characterizing these systems. In this paper, we quantify the trade-off between speed, error, and dissipation using tools from mathematical optimization theory. We characterize the Pareto optimal front for two paradigmatic models of biological error correction: Hopfield's kinetic proofreading model and a ribosome model. We find that error correction processes with more proofreading steps are characterized by better trade-offs. Furthermore, we identify scaling relations between speed, accuracy, and dissipation on the Pareto front.