| A hierarchical exact accelerated stochastic simulation algorithm. | |
| | |
MedLine Citation:
|
PMID: 23231214 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
|
A new algorithm, "HiER-leap" (hierarchical exact reaction-leaping), is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or divide-and-conquer organization of reaction channels into tightly coupled "blocks" and is thereby able to speed up systems with many reaction channels. Like ER-leap, HiER-leap is based on the use of upper and lower bounds on the reaction propensities to define a rejection sampling algorithm with inexpensive early rejection and acceptance steps. But in HiER-leap, large portions of intra-block sampling may be done in parallel. An accept/reject step is used to synchronize across blocks. This method scales well when many reaction channels are present and has desirable asymptotic properties. The algorithm is exact, parallelizable and achieves a significant speedup over the stochastic simulation algorithm and ER-leap on certain problems. This algorithm offers a potentially important step towards efficient in silico modeling of entire organisms. |
| | |
Authors:
|
David Orendorff; Eric Mjolsness |
Related Documents
:
|
12549674 - Predictive qsar modeling based on diversity sampling of experimental datasets for the t... 18328754 - The importance of the domain of applicability in qsar modeling. 17472334 - Qsar analyses of skin penetration enhancers. 14759734 - Qsar modeling of hiv-1 reverse transcriptase inhibitor 2-amino-6-arylsulfonylbenzonitri... 8997544 - Comparing non-hierarchical models: application to non-linear mixed effects modeling. 11590094 - Principal component analysis for clustering gene expression data. |
Publication Detail:
|
Type: Journal Article |
Journal Detail:
|
Title: The Journal of chemical physics Volume: 137 ISSN: 1089-7690 ISO Abbreviation: J Chem Phys Publication Date: 2012 Dec |
Date Detail:
|
Created Date: 2012-12-12 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 0375360 Medline TA: J Chem Phys Country: United States |
Other Details:
|
Languages: eng Pagination: 214104 Citation Subset: IM |
Affiliation:
|
Department of Computer Science, University of California, Irvine, California 92697, USA. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Relaxed active space: Fixing tailored-CC with high order coupled cluster. I.
Next Document: Reducing the effect of Metropolization on mixing times in molecular dynamics simulations.