Hybrid stochastic and deterministic simulations of calcium blips

Rüdiger, S. and Shuai, J.W. and Huisinga, W. and Nagaiah, Ch. and Warnecke, G. and Parker, I. and Falcke, M. (2007) Hybrid stochastic and deterministic simulations of calcium blips. Biophysical Journal, 93 (6). pp. 1847-1857. ISSN 0006-3495

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Intracellular calcium release is a prime example for the role of stochastic effects in cellular systems. Recent models consist of deterministic reaction-diffusion equations coupled to stochastic transitions of calcium channels. The resulting dynamics is of multiple time and spatial scales, which complicates far-reaching computer simulations. In this paper we introduce a novel hybrid scheme that is especially tailored to accurately trace events with essential stochastic variations, while deterministic concentration variables are effciently and accurately traced at the same time. We use finite elements to e±ciently resolve the extreme spatial gradients of concentration variables close to a channel. We describe the algorithmic approach and we demonstrate its efficiency compared to conventional methods. Our single channel model matches experimental data by Mak et al. (PNAS 95 (1998) 15821) and results in intriguing dynamics if calcium is used as charge carrier. Random openings of the channel accumulate in bursts of calcium blips that may be central for the understanding of cellular calcium dynamics.

Item Type: Article
Keywords: Hybrid Stochastic; Deterministic Simulations; Calcium Blips; Calcium signaling; Calcium dynamics; Hamilton Institute.
Academic Unit: Faculty of Science and Engineering > Biology
Faculty of Science and Engineering > Research Institutes > Hamilton Institute
Item ID: 1849
Identification Number: 10.1529/biophysj.106.099879 Biophysical Journal Volume 93 September 2007 1847–1857 1847
Depositing User: Hamilton Editor
Date Deposited: 16 Feb 2010 11:51
Journal or Publication Title: Biophysical Journal
Publisher: Cell Press
Refereed: Yes

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