Abstract
To simulate the spatiotemporal distribution of chemical compounds, we present BioFVM, an open-source reaction-diffusion equation solver using finite volume methods with motivation for biological applications. With various numerical solvers, we can simulate the interaction of dozens of compounds, including growth substrates, drugs, and signaling compounds in 3-D tissues, with cells by treating them as various source/sink terms. BioFVM has linear computational cost scalings and demonstrates first-order accuracy in time and second-order accuracy in space. Beyond simulating the transport of drugs and growth substrates in tissues, the ability to simulate dozens of compounds should make 3-D simulations of multicellular secretomics feasible.
Footnotes
Research supported by University of Southern California (USC) Center for Applied Molecular Medicine (CAMM), the Breast Cancer Research Foundation, the NIH (5U54CA143907, 1R01CA180149), and the USC James H. Zumberge Research and Innovation Fund.
S. H. F., A. G., and P. M. are all with the USC CAMM, 2250 Alcazar St, Rm 240, Los Angeles, CA, 90089. P. M. is the corresponding author. (phone: 310-701-5785; fax: 323-442-2764; e-mail: Paul.Macklin{at}usc.edu). S. H. F. is samuelf{at}usc.edu. A. G. is farzin.ghaffarizadeh{at}cammlab.org.