Computing with metabolic machines

If Turing were a first-year graduate student interested in computers, he would probably migrate into the field of computational biology. During his studies, he presented a work about a mathematical and computational model of the morphogenesis process, in which chemical substances react together. Moreover, a protein can be thought of as a compu-tational element, i.e. a processing unit, able to transform an input into an output signal. Thus, in a biochemical pathway, an enzyme reads the amount of reactants (substrates) and converts them in products. In this work, we consider the biochemical pathway in unicellular organisms (e.g. bacteria) as a living computer, and we are able to program it in order to obtain desired outputs. The genome sequence is thought of as an executable code specified by a set of commands in a sort of ad-hoc low-level programming language. Each combination of genes is coded as a string of bits y ∈ {0, 1}L, each of which represents a gene set. By turning off a gene set, we turn off the chemical reaction associated with it. Through an optimal executable code stored in the “memory ” of bacteria, we are able to simultaneously maximise the concentration of two or more metabolites of interest. Finally, we use the Robustness Analysis and a new Sensitivity Analysis method to investigate both the fragility of the computation carried out by bacteria and the most important entities in the mathematical relations used to model them. 1 Introduction: From Turin