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bioRxiv · 10.1101/035709

Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM

Samuel H Friedman·Ahmadreza Ghaffarizadeh·Paul Macklin
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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.

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Samuel H Friedman, Ahmadreza Ghaffarizadeh, Paul Macklin. 2015-12-30. Simulating multi-substrate diffusive transport in 3-D tissues with BioFVM. https://doi.org/10.1101/035709

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