General transient solution of the one-step master equation in one dimension
File(s)PhysRevE.91.062119.pdf (429.77 KB)
Published version
Author(s)
Smith, S
Shahrezaei, V
Type
Journal Article
Abstract
Exact analytical solutions of the master equation are limited to special cases and exact numerical methods are
inefficient. Even the generic one-dimensional, one-step master equation has evaded exact solution, aside from
the steady-state case. This type of master equation describes the dynamics of a continuous-time Markov process
whose range consists of positive integers and whose transitions are allowed only between adjacent sites. The
solution of any master equation can be written as the exponential of a (typically huge) matrix, which requires
the calculation of the eigenvalues and eigenvectors of the matrix. Here we propose a linear algebraic method
for simplifying this exponential for the general one-dimensional, one-step process. In particular, we prove that
the calculation of the eigenvectors is actually not necessary for the computation of exponential, thereby we
dramatically cut the time of this calculation. We apply our new methodology to examples from birth-death
processes and biochemical networks. We show that the computational time is significantly reduced compared to
existing methods
inefficient. Even the generic one-dimensional, one-step master equation has evaded exact solution, aside from
the steady-state case. This type of master equation describes the dynamics of a continuous-time Markov process
whose range consists of positive integers and whose transitions are allowed only between adjacent sites. The
solution of any master equation can be written as the exponential of a (typically huge) matrix, which requires
the calculation of the eigenvalues and eigenvectors of the matrix. Here we propose a linear algebraic method
for simplifying this exponential for the general one-dimensional, one-step process. In particular, we prove that
the calculation of the eigenvectors is actually not necessary for the computation of exponential, thereby we
dramatically cut the time of this calculation. We apply our new methodology to examples from birth-death
processes and biochemical networks. We show that the computational time is significantly reduced compared to
existing methods
Date Issued
2015-06-16
Date Acceptance
2015-03-07
Citation
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 2015, 91 (6), pp.062119-1-062119-6
ISSN
1063-651X
Publisher
American Physical Society
Start Page
062119-1
End Page
062119-6
Journal / Book Title
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
Volume
91
Issue
6
Copyright Statement
©2015 American Physical Society
Subjects
Science & Technology
Physical Sciences
Physics, Fluids & Plasmas
Physics, Mathematical
Physics
BIOCHEMICAL NETWORKS
BIOLOGICAL-SYSTEMS
MATRIX
APPROXIMATION
DISTRIBUTIONS
KINETICS
COMPUTE
Publication Status
Published
Article Number
062119