Section: New Results

CRN design by program compilation

Participants : Elisabeth Degrand, François Fages, Mathieu Hemery, Wei-Chih Huang [NTU Taiwan] , Sylvain Soliman.

One goal of synthetic biology is to implement useful functions with biochemical reactions, either by reprogramming living cells or programming artificial vesicles. In this perspective, we consider Chemical Reaction Networks (CRN) as a programming language, and investigate the CRN program synthesis problem. Recent work has shown that CRN interpreted by differential equations are Turing-complete and can be seen as analog computers where the molecular concentrations play the role of information carriers. Any real function that is computable by a Turing machine in arbitrary precision can thus be computed by a CRN over a finite set of molecular species. The proof of this result gives a numerical method to generate a finite CRN for implementing a real function presented as the solution of a Polynomial Initial Values Problem (PIVP).

The compilation of high-level imperative programming languages in CRN requires however an efficient implementation of program control flows using threshold functions. The biochemical threshold function is also a crucial component in the biosensor circuits to be deployed in living cells or synthetic vesicles for disease diagnosis. In [5], based on the zero-order ultrasensitivity, we propose an economic biochemical implementation of threshold functions with reconfigurable threshold values. We show that the so-constructed threshold function module well approximates the unit step function and allows robust composition with other function modules for complex computation tasks. This is now implemented in BIOCHAM-4 for the compilation of sequentiality and conditionals in CRNs.