MESH REFINEMENT AND PARALLELIZATION OF VCELL PDE SOLVERS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The project focuses on improving computational efficiency of VCell. This will be achieved by applying adaptive meshes, which allow for more precise modeling of geometry, and by using parallel solvers. Departure from uniform grids and incorporation of parallel solvers in VCell will speed up very large, computationally intensive simulations, particularly of three-dimensional models with multiple spatial scales. The research plan is based on synergistic development of mesh adaptivity and parallel implementation of the solvers, which will take advantage, wherever possible, of available technologies, software, and robust approaches that have been validated by the scientific community. Getting good performance out of available libraries, however, will require extensive testing and evaluation depending on the particular type of problems that need to be solved. The initial phase of the project will include evaluation of PETSc' (Portable, Extensible Toolkit for Scientific computation) parallel solvers and research on current methods for structured mesh refinement.