Numerical solutions of master equation for protein folding kinetics

Yiming Li

doi:10.1109/ICPADS.2005.205

Numerical solutions of master equation for protein folding kinetics

Yiming Li^*

^*Corresponding author for this work

National Chiao Tung University

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

Numerical solution of a master equation involves the calculation of eigenpairs for the corresponding transition matrix. In this paper, we computationally study the folding rate for a kinetics problem of protein folding by solving a largescale eigenvalue problem. Three numerical methods, the implicitly restarted Arnoldi, the Jacobi-Davidson, and the QR methods are applied to solve the corresponding large scale eigenvalue problem of the transition matrix of master equation. Comparison among three methods is performed in terms of the computational efficiency. It is found that the QR method demands tremendous computing resource when the length of sequence L > 10 due to the extremely large size of matrix and CPU time limitation. The Jacobi-Davidson method may encounter convergence issue, for some testing cases with L > 9. The implicitly restarted Arnoldi method is suitable for solving the problem among three solution methods. Numerical examples with various residues are investigated.

Original language	English
Title of host publication	Proceedings - 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005
Editors	J. Ma, L.T. Yang
Pages	351-355
Number of pages	5
DOIs	https://doi.org/10.1109/ICPADS.2005.205
State	Published - 2005
Event	11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005 - Fukuoka, Japan Duration: 20 Jul 2005 → 22 Jul 2005

Publication series

Name	Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS
Volume	2
ISSN (Print)	1521-9097

Conference

Conference	11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005
Country	Japan
City	Fukuoka
Period	20/07/05 → 22/07/05

Access to Document

10.1109/ICPADS.2005.205

Link to publication in Scopus

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Li, Y. (2005). Numerical solutions of master equation for protein folding kinetics. In J. Ma, & L. T. Yang (Eds.), Proceedings - 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005 (pp. 351-355). (Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS; Vol. 2). https://doi.org/10.1109/ICPADS.2005.205

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title = "Numerical solutions of master equation for protein folding kinetics",

abstract = "Numerical solution of a master equation involves the calculation of eigenpairs for the corresponding transition matrix. In this paper, we computationally study the folding rate for a kinetics problem of protein folding by solving a largescale eigenvalue problem. Three numerical methods, the implicitly restarted Arnoldi, the Jacobi-Davidson, and the QR methods are applied to solve the corresponding large scale eigenvalue problem of the transition matrix of master equation. Comparison among three methods is performed in terms of the computational efficiency. It is found that the QR method demands tremendous computing resource when the length of sequence L > 10 due to the extremely large size of matrix and CPU time limitation. The Jacobi-Davidson method may encounter convergence issue, for some testing cases with L > 9. The implicitly restarted Arnoldi method is suitable for solving the problem among three solution methods. Numerical examples with various residues are investigated.",

author = "Yiming Li",

year = "2005",

doi = "10.1109/ICPADS.2005.205",

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Li, Y 2005, Numerical solutions of master equation for protein folding kinetics. in J Ma & LT Yang (eds), Proceedings - 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005. Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS, vol. 2, pp. 351-355, 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005, Fukuoka, Japan, 20/07/05. https://doi.org/10.1109/ICPADS.2005.205

Numerical solutions of master equation for protein folding kinetics. / Li, Yiming.

Proceedings - 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005. ed. / J. Ma; L.T. Yang. 2005. p. 351-355 (Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS; Vol. 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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