Numerical solutions of master equation for protein folding kinetics

Yiming Li*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 languageEnglish
Title of host publicationProceedings - 11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005
EditorsJ. Ma, L.T. Yang
Pages351-355
Number of pages5
DOIs
StatePublished - 2005
Event11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005 - Fukuoka, Japan
Duration: 20 Jul 200522 Jul 2005

Publication series

NameProceedings of the International Conference on Parallel and Distributed Systems - ICPADS
Volume2
ISSN (Print)1521-9097

Conference

Conference11th International Conference on Parallel and Distributed Systems Workshops, ICPADS 2005
CountryJapan
CityFukuoka
Period20/07/0522/07/05

Fingerprint Dive into the research topics of 'Numerical solutions of master equation for protein folding kinetics'. Together they form a unique fingerprint.

  • Cite this

    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