QSB: Multiscale Modeling of Gene Regulatory Modules

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Kaznessis0425882This research focuses on the integration of a number of simulation algorithms into a seamless multiscale algorithm for modeling biological regulatory processes, which extend from a stochastic low-copy number regime to a high-concentration 'continuous' regime. This work builds on important earlier work, particularly that of Gillespie. The simulation algorithms which will be integrated are: a stochastic simulation algorithm; a chemical Langevin algorithm, to deal with conditions resulting in Gaussian fluctuations about a mean; and a multiscale deterministic simulation algorithm, to manage the continuous 'high concentration' range. An important goal of these studies is the creation of a 'platform' from which to approach in silico design of biologically interesting gene expression systems. These systems are described in some detail in the proposal, and include: bistable switching; simulation of oscillatory and biochemical systems; and multiscale deterministic modeling of metabolism.