Section: New Results

Analog computation in the cell: specifications, compilation into biochemical reactions and computational complexity

Participants : François Fages, Guillaume Le Guludec.

The continuous nature of many protein interactions leads us to consider mixed analog-digital computation methods, for which 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, and present a compiler of behavioural specifications into biochemical reactions which can be compared to natural circuits acquired through evolution. We illustrate this approach through the example of the MAPK signaling module which has a function of analog-digital converter in the cell, and through the cell cycle control.

The biochemical compiler is implemented in BIOCHAM v4.0 which will be soon released. We plan to use it in the ANR-MOST project BIOPSY on “Biochemical Programming” for the design of artificial biosensors and the programming of (non-living) protocells in collaboration with Franck Molina, CNRS Sys2diag lab, Montpellier.