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Figure 5 | BMC Systems Biology

Figure 5

From: URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Figure 5

Geometry and mesh for a model of a neuron. The neuron geometry (A) is based on a artistic CAD rendering generated with the public domain version of the software Blender ( In order to conduct simulations in this geometry, the model was exported in the STL surface mesh format, imported into the open-source meshing package Gmsh [31], where the boundary was re-parametrized and the domain subsequently meshed with a volume mesh in 3D. The resulting mesh was then converted into a Comsol Multiphysics 3.5a model to serve as a geometry description for the URDME model. Assembly of active transport jump rate constants are conducted by URDME on the unstructured mesh shown in (B). For a mathematical background on how to obtain these constants on the unstructured mesh, see [35]. URDME’s capability to use an unstructured mesh made up of tetrahedral and triangular elements is of vital importance in order to be able to resolve the complex geometry of the neuron.

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