This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Virtual Cell default linear solver using the preconditioned conjugate gradient method (PCG) has been extended to include a more general minimal residual algorithm (GMRES), which is applicable to non-symmetrical matrices. The code linking the Virtual Cell C++ library to the GMRES solver from PCGPAK has been written and thoroughly tested. Several numerical algorithms for discretization of reaction-diffusion-advection equations (central difference, upwind, and hybrid) have been implemented. In all cases, the finite volume conservative scheme was used. We have developed a set of examples that are used for thorough testing the solver in 1-, 2-, and 3 dimensions. The hybrid method has been chosen as default. The new capability to model advection along with diffusion and reactions can be applied to study competition of various molecular motors driving organelles along cytoskeletal filaments. Automatic code generation for this type of applications is being tested.
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