The Virtual Cell Project
University of Connecticut Health Center, University of Connecticut
(September 10, 2012 3:00 PM - 3:50 PM)
The shape of a cell, the sizes of subcellular compartments and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior. This talk describes how these spatial features can be included in mechanistic mathematical models of cell biology. The Virtual Cell (VCell) computational modeling and simulation software is designed for spatial modeling of cellular reaction-diffusion systems. VCell facilitates choices between physical formulations that implicitly or explicitly account for cell geometry and between deterministic vs, stochastic formulations for biochemical reactions. VCell allows modelers to separately define the model physiology, which includes the molecules, their reactions and membrane transport processes. As a first step toward constructing a spatial model, the geometry needs to be specified and associated with the molecules, reactions and membrane flux processes of the reaction network. Initial conditions, diffusion coefficients, velocities and boundary conditions complete the specifications required to define the mathematics of the model. The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically include a variety of ODE, PDE, and probabilistic solvers. A study of actin dynamics provides an example of the insights that can be gained in interpreting experimental results through the application of spatial modeling.