A Low Dimensional Approximation For Competence In Bacillus Subtilis

An Nguyen, Adam Prugel-Bennett, Srinandan Dasmahapatra
2016 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
The behaviour of a high dimensional stochastic system described by a Chemical Master Equation (CME) depends on many parameters, rendering explicit simulation an inefficient method for exploring the properties of such models. Capturing their behaviour by low-dimensional models makes analysis of system behaviour tractable. In this paper, we present low dimensional models for the noise-induced excitable dynamics in Bacillus subtilis, whereby a key protein ComK, which drives a complex chain of
more » ... ions leading to bacterial competence, gets expressed rapidly in large quantities (competent state) before subsiding to low levels of expression (vegetative state). These rapid reactions suggest the application of an adiabatic approximation of the dynamics of the regulatory model that, however, lead to competence durations that are incorrect by a factor of 2. We apply a modified version of an iterative functional procedure that faithfully approximates the time-course of the trajectories in terms of a 2-dimensional model involving proteins ComK and ComS. Furthermore, in order to describe the bimodal bivariate marginal probability distribution obtained from the Gillespie simulations of the CME, we introduce a tunable multiplicative noise term in a 2-dimensional Langevin model whose stationary state is described by the time-independent solution of the corresponding Fokker-Planck equation.
doi:10.1109/tcbb.2015.2440275 pmid:27045827 fatcat:yda24ljzsrbsrpb3kqqjnqmlo4