Sparse grids and hybrid methods for the chemical master equation
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Hegland, Markus; Hellander, Andreas; Lotstedt, Per
Description
The direct numerical solution of the chemical master equation (CME) is usually impossible due to the high dimension of the computational domain. The standard method for solution of the equation is to generate realizations of the chemical system by the stochastic simulation algorithm (SSA) by Gillespie and then taking averages over the trajectories. Two alternatives are described here using sparse grids and a hybrid method. Sparse grids, implemented as a combination of aggregated grids are used...[Show more]
dc.contributor.author | Hegland, Markus | |
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dc.contributor.author | Hellander, Andreas | |
dc.contributor.author | Lotstedt, Per | |
dc.date.accessioned | 2015-12-07T22:49:36Z | |
dc.identifier.issn | 0006-3835 | |
dc.identifier.uri | http://hdl.handle.net/1885/26834 | |
dc.description.abstract | The direct numerical solution of the chemical master equation (CME) is usually impossible due to the high dimension of the computational domain. The standard method for solution of the equation is to generate realizations of the chemical system by the stochastic simulation algorithm (SSA) by Gillespie and then taking averages over the trajectories. Two alternatives are described here using sparse grids and a hybrid method. Sparse grids, implemented as a combination of aggregated grids are used to address the curse of dimensionality of the CME. The aggregated components are selected using an adaptive procedure. In the hybrid method, some of the chemical species are represented macroscopically while the remaining species are simulated with SSA. The convergence of variants of the method is investigated for a growing number of trajectories. Two signaling cascades in molecular biology are simulated with the methods and compared to SSA results. | |
dc.publisher | Springer | |
dc.source | BIT: Numerical mathematics (Lisse) | |
dc.subject | Keywords: Hybrid method; Master equation; Sparse grids; Stochastic chemical kinetics | |
dc.title | Sparse grids and hybrid methods for the chemical master equation | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 48 | |
dc.date.issued | 2008 | |
local.identifier.absfor | 010301 - Numerical Analysis | |
local.identifier.ariespublication | u4085724xPUB47 | |
local.type.status | Published Version | |
local.contributor.affiliation | Hegland, Markus, College of Physical and Mathematical Sciences, ANU | |
local.contributor.affiliation | Hellander, Andreas, Uppsala University | |
local.contributor.affiliation | Lotstedt, Per, Uppsala University | |
local.description.embargo | 2037-12-31 | |
local.bibliographicCitation.issue | 2 | |
local.bibliographicCitation.startpage | 265 | |
local.bibliographicCitation.lastpage | 283 | |
local.identifier.doi | 10.1007/s10543-008-0174-z | |
dc.date.updated | 2015-12-07T12:10:00Z | |
local.identifier.scopusID | 2-s2.0-49749127994 | |
local.identifier.thomsonID | 000258527500007 | |
Collections | ANU Research Publications |
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