Java-based modeling of the actin polymerization cycle

Abstract

This thesis project combines work on two aspects· of a project entitled "A Mechanistic Model of the Actin Cycle" [ 1,2]. This project uses accumulated biochemical research to write a broad mathematical model that describes the effects of regulatory proteins (profilin, beta-thymosin, cofilin, and capping protein) on the steady-state actin cycle. The model necessitates the simultaneous solving of 90-330 differential equations and 51-171 additional equations. One object of this thesis was to prove that this model could be run on JSim, a modeling architecture developed at the University of Washington, to obtain the same results as McGrath et al calculated using Matlab. The theory behind using JSim was that it would be faster and more accessible, since JSim is Java-based and contains all the necessary software to run on various platforms. This project proved that the equations could be run quickly with JSim. It also highlighted some of the drawbacks of JSim, such as heavy demand on the processor. A second object of this thesis was to provide an independent evaluation of the mathematical model and correct mistakes in the original draft. Several errors were uncovered and the corrected results now appear in the paper submitted to The Biophysical Journal [2].