BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.

ABSTRACT:

Motivation

Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology.

Results

We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-

SUBMITTER: Ghaffarizadeh A 

PROVIDER: S-EPMC4824128 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature