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Spice simulation of intracellular transport: Free diffusion
Author(s) -
Vasilescu Gabriel,
Chen Luonan
Publication year - 2011
Publication title -
asian journal of control
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.769
H-Index - 53
eISSN - 1934-6093
pISSN - 1561-8625
DOI - 10.1002/asjc.384
Subject(s) - diffusion , resistor , spice , steady state (chemistry) , computer science , analogy , statistical physics , process (computing) , mechanism (biology) , work (physics) , scale (ratio) , biological system , simulation , physics , chemistry , electronic engineering , engineering , electrical engineering , thermodynamics , voltage , linguistics , philosophy , quantum mechanics , biology , operating system
Diffusion is the main mechanism to transport substances (e.g. amino‐acids and proteins) within a cell. In any biological process the number of molecules is too small to satisfy the statistical assumptions implicit in diffusion theory. As an alternative, various methods to simulate diffusion have been developed, which are rather microscopic. Consequently, the time‐scale and volume simulated are forcefully restricted and the final steady‐state cannot be reached. In this paper we propose a macroscopic method, based on the analogy established between diffusing particles and the free electrons moving in a resistor–capacitor ( RC ) circuit. The purpose of this work is to extend simulation beyond the actual limits of microscopic approaches and thus to obtain additional insight into the essential mechanism of biological systems. Analysis is performed with a publicly‐released package (PSPICE). A procedure to build the electrical model and to fit its parameters is proposed. Simulation yields time‐evolution of particle densities including the final steady‐state and transport efficiency evaluation. Our method equally allows accounting for the presence of a crowded area in the diffusion pathway, the impact of several bursts of fabricated protein, as well as the case of transport simultaneously occurring on many directions. Several examples and a case study are provided to illustrate the effectiveness of our approach. Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society