The investigators propose to develop """"""""Virtual Cell,"""""""" a simulation framework for building complex cell models based on a hierarchical assembly of molecules, reaction mechanisms, and their associated intracellular structures. The numerical simulation is based on the finite volume method which permits a spatially heterogenous collection volume elements (compartments). The geometries of the compartments are derived directly from experimental microscope images. The partial differential equations of electrodiffusion, plus source terms corresponding to reactions, are solved for each chemical species in each volume element. The framework integrates continuous and discrete mathematical treatments. Comparison of simulation results and experimentally observed behavior is facilitated because the microscopy data and simulation model are mapped onto the same geometry. The three specific aims of the computational infrastructure project are to 1) develop continuous and discrete modeling descriptions o f cell processes and geometries, integrated in a single computational framework, 2) build a phenomenon-level web-based user interface, and 3) parallelize the code and investigate efficiency and portability issues.
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