Computational study of p53 regulation via the chemical master equation

A stochastic model of cellular p53 regulation was established in Leenders, and Tuszynski (2013 Front. Oncol. 3 1-16) to study the interactions of p53 with MDM2 proteins, where the stochastic analysis was done using a Monte Carlo approach. We revisit that model here using an alternative scheme, which...

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Bibliographic Details
Published in:Physical biology Vol. 13; no. 3; p. 035001
Main Authors: Vo, Huy D, Sidje, Roger B
Format: Journal Article
Language:English
Published: England 29.04.2016
Subjects:
Algorithms
Computer Simulation
Models, Chemical
Proto-Oncogene Proteins c-mdm2 - chemistry
Proto-Oncogene Proteins c-mdm2 - metabolism
Stochastic Processes
Tumor Suppressor Protein p53 - chemistry
Tumor Suppressor Protein p53 - metabolism
ISSN:1478-3975, 1478-3975
Online Access:Get more information
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Summary:A stochastic model of cellular p53 regulation was established in Leenders, and Tuszynski (2013 Front. Oncol. 3 1-16) to study the interactions of p53 with MDM2 proteins, where the stochastic analysis was done using a Monte Carlo approach. We revisit that model here using an alternative scheme, which is to directly solve the chemical master equation (CME) by an adaptive Krylov-based finite state projection method that combines the stochastic simulation algorithm with other computational strategies, namely Krylov approximation techniques to the matrix exponential, divide and conquer, and aggregation. We report numerical results that demonstrate the extend of tackling the CME with this combination of tools.
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ISSN:1478-3975
1478-3975
DOI:10.1088/1478-3975/13/3/035001