Designing simulations to investigate reactions inside the cells

Marcio Duarte Albasini Mourao
Mathematical Biosciences Institute, The Ohio State University

(January 30, 2014 10:20 AM - 11:15 AM)

Designing simulations to investigate reactions inside the cells

Abstract

Although extensively applied to model biochemical reactions inside cells, the law of mass action assumes that reactions occur in homogeneous, well-stirred volumes. This is inconsistent with the heterogeneous environment that characterizes intracellular reactions. 

In fact, reaction kinetics can be either classical (following the law of mass action) or non-classical (following Kopelman's fractal-like kinetics). Both cases are likely to occur, but it is not clear under what conditions one obtains these reaction types. In this talk, I will discuss the use of Monte-Carlo simulations to investigate kinetic laws in in vivo conditions. Within the context of a two dimensional lattice-based simulation of the Michaelis-Menten mechanism in diffusion-limited conditions, I will also discuss the effect of obstacle density and size on reactant diffusion and rate coefficients. We show that obstacle density and size affect diffusion, first- and second- order rates. We also show that particle rotations and weak force interactions among particles lead to a significant decay in the fractal-like kinetics. All together, these results suggest that the effects of fractal-like kinetics disappear under less restricted conditions than previously believed.