The chemical Langevin equation for biochemical systems in dynamic environments

Abstract

Modeling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. Many of the approaches developed so far capture temporal fluctuations due to the inherent stochasticity of the biophysical processes, referred to as intrinsic noise. Stochastic fluctuations, however, predominantly stem from the interplay of the network with many other - and mostly unknown - fluctuating processes, as well as with various random signals arising from the extracellular world; these sources contribute extrinsic noise. Here, we provide a computational simulation method to probe the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. We deve..