dorsal/arxiv
View SchemaA "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics
| Authors | Leonard A. Harris, Paulette Clancy |
|---|---|
| Categories | |
| ArXiv ID | physics/0601217 |
| URL | https://arxiv.org/abs/physics/0601217 |
| DOI | 10.1063/1.2354085 |
| Journal | J. Chem. Phys. 125 (2006) 144107 |
Abstract
We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.
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"abstract": "We present a novel multiscale simulation approach for modeling stochasticity\nin chemical reaction networks. The approach seamlessly integrates\nexact-stochastic and \"leaping\" methodologies into a single \"partitioned\nleaping\" algorithmic framework. The technique correctly accounts for stochastic\nnoise at significantly reduced computational cost, requires the definition of\nonly three model-independent parameters and is particularly well-suited for\nsimulating systems containing widely disparate species populations. We present\nthe theoretical foundations of partitioned leaping, discuss various options for\nits practical implementation and demonstrate the utility of the method via\nillustrative examples.",
"arxiv_id": "physics/0601217",
"authors": [
"Leonard A. Harris",
"Paulette Clancy"
],
"categories": [
"physics.chem-ph",
"physics.comp-ph",
"q-bio.QM"
],
"doi": "10.1063/1.2354085",
"journal_ref": "J. Chem. Phys. 125 (2006) 144107",
"title": "A \"partitioned leaping\" approach for multiscale modeling of chemical reaction dynamics",
"url": "https://arxiv.org/abs/physics/0601217"
},
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