Analytic framework for stochastic binary biological switches

Abstract

We propose an analytic solution for the stochastic dynamics of a binary biological switch, defined as a DNA unit with two mutually exclusive configurations, each one triggering the expression of a different gene. Such a device could be used as a memory unit for biological computing systems designed to operate in noisy environments. We discuss a recent implementation of an exclusive switch in living cells, the recombinase addressable data (RAD) module. In order to understand the behavior of a RAD module we compute the exact time dependent distributions of the two expressed genes starting in one state and evolving to another asymptotic state. We consider two operating regimes of the RAD module: fast and slow stochastic switching. The fast regime is \"aggregative\" and produces unimodal distributions, whereas the slow regime is \"separative\" and produces bimodal distributions. Both regimes can serve to prepare pure memory states when all cells are expressing the same gene. The slow regime can also separate mixed states by producing two sub-populations each one expressing a different gene. Our model provides a simplified, general phenomenological framework for studying biological memory devices and our analytic solution can be further used to clarify theoretical concepts in bio-computation and for optimal design in synthetic biology.