Chemical relaxation oscillator designed to control molecular computation

TL;DR

This paper introduces a 4-dimensional chemical relaxation oscillator model that generates clock signals to regulate molecular computation modules, enabling more complex biochemical calculations.

Contribution

The work presents a novel chemical oscillator design for controlling module sequencing and termination in molecular computation systems.

Findings

Dynamical analysis of the oscillator model

Control methods for period and order of clock signals

Loop control and termination strategies for molecular computations

Abstract

Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make them alternate spontaneously. Our work takes the design of chemical clock signals as a solution and presents a $4$-dimensional chemical oscillator model based on relaxation oscillation to generate a pair of symmetric clock signals for two-module regulation. We give detailed dynamical analysis of the model and discuss how to control the period and occurrence order of clock signals. We also demonstrate the loop control of molecular computations and provide termination strategy for them. We can expect that our design for module regulation and loop termination will help advance the embedding of more complicate calculations into biochemical environments.