Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell

This chapter considers IT perspective in seeking to understand how computation is carried out in the cell to maintain itself in its environment, process signals and make the decisions that determine its fate. The continuous nature of many protein interactions leads authors to consider mixed analog-digital computation models, for which recent results in the theory of analog computability and complexity establish fundamental links with classical programming. The chapter derives from these results a compiler of behavioral specifications into biochemical reactions, which can be compared to natural circuits acquired through evolution. It illustrates this approach through the example of the mitogen-activated protein kinase (MAPK) signaling module, which has an analog-digital converter function in the cell, and through the cell cycle control. The time logic CTL provides a very powerful expression language for the analysis of the Boolean dynamics of a reaction system.