Authors: Yiming Li
Addresses: Department of Communication Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
Abstract: The 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 large-scale 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 the 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 issues, for some testing cases with L > 9. Among the three solution methods the implicitly restarted Arnoldi method is suitable for solving the problem. Numerical examples with various residues are investigated.
Keywords: protein folding; kinetics; master equation; numerical methods; eigenvalues; transition matrix; QR; Arnoldi; Jacobi-Davidson; bioinformatics research; bioinformatics applications; high performance computing.
International Journal of Bioinformatics Research and Applications, 2006 Vol.2 No.4, pp.420 - 429
Published online: 05 Oct 2006 *Full-text access for editors Access for subscribers Purchase this article Comment on this article