CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012 vol.9 Issue No.01 - January/February

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Issue No.01 - January/February (2012 vol.9)

pp: 40-51

Chong Wang , Biomed. Sci. Res. Inst., Univ. of Ulster, Coleraine, UK

P. Beyerlein , Dept. of Bioinf., Tech. Univ. Wildau, Wildau, Germany

H. Pospisil , Dept. of Bioinf., Tech. Univ. Wildau, Wildau, Germany

A. Krause , Dept. of Bioinf., Bingen Univ. of AP, Bingen am Rhein, Germany

C. Nugent , Comput. Sci. Res. Inst., Univ. of Ulster, Newtownabbey, Jordan

W. Dubitzky , Comput. Sci. Res. Inst., Univ. of Ulster, Newtownabbey, Jordan

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.84

ABSTRACT

Characterization of the kinetic and conformational properties of channel proteins is a crucial element in the integrative study of congenital cardiac diseases. The proteins of the ion channels of cardiomyocytes represent an important family of biological components determining the physiology of the heart. Some computational studies aiming to understand the mechanisms of the ion channels of cardiomyocytes have concentrated on Markovian stochastic approaches. Mathematically, these approaches employ Chapman-Kolmogorov equations coupled with partial differential equations. As the scale and complexity of such subcellular and cellular 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.

INDEX TERMS

Proteins, Kinetic theory, Mathematical model, Equations, Biomembranes, Numerical models, Heuristic algorithms,Markov model., Cardiomyocyte, arrhythmia, channel protein, conformation, kinetic pathway, differential equations

CITATION

Chong Wang, P. Beyerlein, H. Pospisil, A. Krause, C. Nugent, W. Dubitzky, "An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.9, no. 1, pp. 40-51, January/February 2012, doi:10.1109/TCBB.2011.84REFERENCES