An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes

Chong Wang, Peter Beyerlein, Heike Pospisil, Antje Krause, Chris D Nugent, W Dubitzky

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Characterization of the kinetic and conformational properties of channel proteins is a crucial element in the integrative studyof congenital cardiac diseases. The proteins of the ion channels of cardiomyocytes represent an important family of biologicalcomponents determining the physiology of the heart. Some computational studies aiming to understand the mechanisms of the ionchannels of cardiomyocytes have concentrated on Markovian stochastic approaches. Mathematically, these approaches employChapman-Kolmogorov equations coupled with partial differential equations. As the scale and complexity of such subcellular andcellular models increases, the balance between efficiency and accuracy of algorithms becomes critical. We have developed a novel two-stage splitting algorithm to address efficiency and accuracy issues arising in such modeling and simulation scenarios. Numerical experiments were performed based on the incorporation of our newly developed conformational kinetic model for the rapid delayed rectifier potassium channel into the dynamic models of human ventricular myocytes. Our results show that the new algorithm significantly outperforms commonly adopted adaptive Runge-Kutta methods. Furthermore, our parallel simulations with coupled algorithms for multicellular cardiac tissue demonstrate a high linearity in the speedup of large-scale cardiac simulations.
LanguageEnglish
Pages40-51
JournalIEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,
Volume9
Issue number1
DOIs
Publication statusPublished - Jan 2012

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Proteins
Kinetics
Runge Kutta methods
Physiology
Partial differential equations
Potassium
Dynamic models
Tissue
Ions
Experiments

Cite this

Wang, Chong ; Beyerlein, Peter ; Pospisil, Heike ; Krause, Antje ; Nugent, Chris D ; Dubitzky, W. / An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes. In: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,. 2012 ; Vol. 9, No. 1. pp. 40-51.
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An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes. / Wang, Chong; Beyerlein, Peter; Pospisil, Heike; Krause, Antje; Nugent, Chris D; Dubitzky, W.

In: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Vol. 9, No. 1, 01.2012, p. 40-51.

Research output: Contribution to journalArticle

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