A Python Framework for Reaction--Diffusion--Chemotaxis Simulations on One-Dimensional Network Geometries
This provides a tool for researchers in fields like microfluidic organ-on-chip devices and vascular networks, but it is incremental as it applies an existing method to a specific domain.
The authors tackled the problem of simulating biological transport phenomena on graph-like geometries by developing BioNetFlux, an open-source Python framework for numerical simulation of coupled PDEs on one-dimensional networks, using the Hybridized Discontinuous Galerkin method.
We present BioNetFlux, an open-source Python framework for the numerical simulation of coupled systems of partial differential equations (PDEs) on one-dimensional multi-arc networks by the Hybridized Discontinuous Galerkin method. Its design targets biological transport phenomena on graph-like geometries that arise naturally in microfluidic organ-on-chip (OoC) devices, vascular networks, and in-vitro cell-migration assays.