کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
519866 867687 2009 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
D-leaping: Accelerating stochastic simulation algorithms for reactions with delays
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نرم افزارهای علوم کامپیوتر
پیش نمایش صفحه اول مقاله
D-leaping: Accelerating stochastic simulation algorithms for reactions with delays
چکیده انگلیسی

We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Computational Physics - Volume 228, Issue 16, 1 September 2009, Pages 5908–5916
نویسندگان
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