RT Journal Article
SR Electronic
T1 Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 035709
DO 10.1101/035709
A1 Samuel H. Friedman
A1 Ahmadreza Ghaffarizadeh
A1 Paul Macklin
YR 2015
UL http://biorxiv.org/content/early/2015/12/30/035709.abstract
AB 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.