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Section: Research Program

Mixed Analog-Digital Computation with Biochemical Reactions

The continuous nature of many protein interactions leads us to consider models of analog computation, and in particular, the recent results in the theory of analog computability and complexity obtained by Amaury Pouly (Amaury Pouly, “Continuous models of computation: from computability to complexity”, PhD Thesis, Ecole Polytechnique, Nov. 2015.) and Olivier Bournez, establish fundamental links with digital computation. In [18], we derive from these results a Turing completeness result for elementary reaction systems (without polymerization) under the differential semantics. The proof of this result shows how mathematical functions described by Ordinary Differential Equations, namely by Polynomial Initial Value Problems (PIVP), can be compiled into elementary biochemical reactions, furthermore with a notion of analog computation complexity defined as the length of the trajectory to reach a given precision on the result. This opens a whole research avenue to analyze natural circuits in Systems Biology, transform behavioural specifications into biochemical reactions for Synthetic Biology, and compare artificial circuits with natural circuits acquired through evolution, from the novel point of view of analog computation complexity.