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Systematic computation of non-linear cellular and molecular dynamics with low-power cytomimetic circuits: A simulation study

Title: Systematic computation of non-linear cellular and molecular dynamics with low-power cytomimetic circuits: A simulation study
Authors: Papadimitriou, KI
Stan, G-B
Drakakis, EM
Item Type: Journal Article
Abstract: This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented.
Issue Date: 5-Feb-2013
Date of Acceptance: 3-Dec-2012
URI: http://hdl.handle.net/10044/1/63623
DOI: https://dx.doi.org/10.1371/journal.pone.0053591
ISSN: 1932-6203
Publisher: Public Library of Science (PLoS)
Journal / Book Title: PLoS ONE
Volume: 8
Issue: 2
Copyright Statement: © 2013 Papadimitriou et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Sponsor/Funder: Engineering & Physical Science Research Council (EPSRC)
Funder's Grant Number: EP/G036004/1
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Computer Simulation
Models, Theoretical
Molecular Dynamics Simulation
MD Multidisciplinary
General Science & Technology
Publication Status: Published
Article Number: e53591
Online Publication Date: 2013-02-05
Appears in Collections:Bioengineering
Faculty of Engineering