A compact synchronous cellular model of nonlinear calcium dynamics: simulation and FPGA synthesis results
File(s)hamid_1_spiral.pdf (30.01 MB)
Accepted version
Author(s)
Soleimani, H
Drakakis, EM
Type
Journal Article
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.
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.
Date Issued
2017-05-23
Date Acceptance
2016-11-28
Citation
IEEE Transactions on Biomedical Circuits and Systems, 2017, 11 (3), pp.703-713
ISSN
1932-4545
Publisher
Institute of Electrical and Electronics Engineers (IEEE)
Start Page
703
End Page
713
Journal / Book Title
IEEE Transactions on Biomedical Circuits and Systems
Volume
11
Issue
3
Copyright Statement
© 2016 EU. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Subjects
Science & Technology
Technology
Engineering, Biomedical
Engineering, Electrical & Electronic
Engineering
Calcium induced calcium releasedmodel (CICR)
CytoMimetic
field programable gate array (FPGA)
synchronous cellular calcium model
SPIKING NEURONS
NETWORK
Electrical & Electronic Engineering
0903 Biomedical Engineering
0906 Electrical And Electronic Engineering
Publication Status
Published