Accurate control to run and stop chemical reactions via relaxation oscillators

Abstract

Regulation of multiple reaction modules is quite common in molecular computation and synthetic genetic circuits through chemical reactions, as is always a headache for that sequential execution of modules goes against the intrinsically parallel nature of chemical reactions. Precisely switching multiple reaction modules both on and off acts as the core role in programming chemical reaction systems. Unlike setting up physical compartments or adding human intervention signals, we adopt the idea of chemical oscillators based on relaxation oscillation, and assign corresponding clock signal components into the modules to be regulated as catalysts. We mainly demonstrate our design process of oscillator model under the regulation task of three modules, and provide a suitable approach for automatic loop termination of the whole system. Analysis and numerical simulation are directly based on dynamical equations of the oscillator model, which can be translated into corresponding chemical reaction networks through mass-action kinetics.