A compact synchronous cellular model of nonlinear calcium dynamics: simulation and FPGA synthesis results

Abstract

Recent studies have demonstrated that calcium is a widespread intracellular ion that controls a wide range of temporal dynamics in the mammalian body. The simulation and validation of such studies us- ing experimental data would bene t from a fast large scale simulation and modelling tool. This paper presents a compact and fully recon gurable cellular calcium model capable of mimicking Hopf bifurcation phenomenon and various nonlinear responses of the biological calcium dynamics. The proposed cellular model is synthesized on a digital platform for a single unit and a network model. Hardware synthesis, physical implementation on FPGA, and theoretical analysis con rm that the proposed cellular model can mimic the biological calcium behaviors with considerably low hardware overhead. The approach has the potential to speed up large{scale simulations of slow intracellular dynamics by sharing more cellular units in real{time. To this end, various networks constructed by pipelining 10k to 40k cellular calcium units are compared with an equivalent simulation run on a standard PC workstation. Results show that the cellular hardware model is, on average, 83 times faster than the CPU version.