Finite Element Procedures for Enzyme, Chemical Reaction and 'In-Silico' Genome Scale Networks

Abstract

The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite elements method (FEM) is at the state-of-art engineering multi-physics simulation system, with tools such as Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD). Although FEA and CFD are currently applied to bioreactor design, most simulations are restricted to the multi-physics capabilities of the existing sofware packages. This manuscript is a contribution for the consolidation of FEM in computational biotechnology, by presenting a comprehensive review of finite element procedures of the most common enzymatic mechanisms found in biotechnological processes, such as, enzyme activation, Michaelis Menten, competitive inhibition, non-competitive inhibition, anti-competitive inhibition, competition by substrate, sequential random mechanism, ping-pong bi-bi and Theorel-Chance. Most importantly, the manuscript opens the possibility for the use of FEM in conjunction with {\guillemotleft}in-silico{\guillemotright} models of metabolic networks, as well as, chemical networks in order to simulate complex bioprocesses in biotechnology, putting emphasis into flux balance analysis, pheno-metabolomics space exploration in time and space, overcoming the limitations of assuming chemostat conditions in systems biology computations.