Digital logic with molecular reactions

This paper presents a methodology for implementing digital logic with molecular reactions based on a bistable mechanism for representing bits. The value of a bit is not determined by the concentration of a single molecular type; rather, it is the comparison of the concentrations of two complementary types that determines if the bit is '0' or '1'. This mechanism is robust: any small perturbation or leakage in the concentrations quickly gets cleared out and the signal value is not affected. Based on this representation for bits, a constituent set of logical components are implemented. These include combinational components - AND, OR, NOR, and XOR - as well as sequential components - D latches and D flip-flops. Using these components, three full-fledged design examples are given: a square-root unit, a binary adder and a linear feedback shift register. DNA-based computation via strand displacement is the target experimental chassis. The designs are validated through simulations of the chemical kinetics. The simulations show that the molecular systems compute digital functions accurately and robustly.