Verilog-A compact space-dependent model for biology

We recently demonstrated that it is possible to model and to simulate biological functions using hardware description languages (and associated simulators) traditionally used for micro-electronics. The main drawback of these languages is that they do not support partial differential equations. However, for several applications in biology, space-dependent quantities are unavoidable. This paper deals with a new approach to address these problems. It is based on previous investigations on electro-thermal simulations in integrated circuits. The tool is composed of four main parts: a mesher that divides space into small cubes (or squares in 2D), a set of interconnected biological models, a SPICE simulator that handles these models and a Python script that interfaces the different tools. Simulation results obtained with our tool are compared with experimental data on a specific case. Results are in good accordance from a qualitative viewpoint.