About: Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

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article by Muruhan Rathinam et al published 22 December 2003 in Journal of Chemical Physics

Attributes	Values
rdf:type	Item
description	artículu científicu (ast) wetenschappelijk artikel (nl) наукова стаття, опублікована в грудні 2003 (uk) article scientifique publié en 2003 (fr) im Dezember 2003 veröffentlichter wissenschaftlicher Artikel (de) article by Muruhan Rathinam et al published 22 December 2003 in Journal of Chemical Physics (en)
publication date	wds:Q57276560-73014424-9226-4273-8919-F5F2E7E77301
publication date	2003-12-22 00:00:00Z (xsd:dateTime)
language of work or name	wds:Q57276560-197C503D-8137-481E-B6DA-CBCE5BD239EE
language of work or name	English
cites work	wds:Q57276560-0C5DCC92-0296-47F7-B846-08B3140E2414 wds:Q57276560-5BBB0C38-11A5-4E14-8175-0B3B99ACE3DE wds:Q57276560-8E46B8A6-5D7D-42A7-9CFE-7986712D41A7 wds:Q57276560-92DE0DD6-177D-4808-9F85-FB338A1267EE wds:Q57276560-9E682C85-803F-4A97-832F-EF98F94696AF wds:Q57276560-D9059CB2-5648-4657-9A17-D56E345EA4B2 wds:Q57276560-EBDA086E-782F-49E8-8079-FA913C60F802
cites work	The chemical Langevin equation A general method for numerically simulating the stochastic time evolution of coupled chemical reactions Stochastic mechanisms in gene expression Approximate accelerated stochastic simulation of chemically reacting systems It's a noisy business! Genetic regulation at the nanomolar scale Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels Genetic networks. Small numbers of big molecules
author name string	wds:Q57276560-C29BFDBA-9A09-47A0-96CB-A1D76FF41B49 wds:Q57276560-DD4742AA-5C42-46BE-83D3-643F33C9B07F wds:Q57276560-F6C65FE9-29A9-42D8-B033-E22EB0D11DD4
author name string	Yang Cao Muruhan Rathinam Daniel T. Gillespie
rdfs:label	Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (en) Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (nl)
skos:prefLabel	Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (en) Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (nl)
name	Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (en) Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (nl)
author	wds:Q57276560-4E00B855-7AEB-4428-87A6-86368E6EB7F3
author	Linda Petzold
title	wds:Q57276560-13C35A58-87C8-47F0-BC9D-5F4FE7DD7983
title	Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method (en)
page(s)	wds:Q57276560-A97B31B6-5D40-4EEC-82E9-36ED57665AEC
page(s)	12784-12794
instance of	wds:Q57276560-9F6BF502-CAF4-4A65-8770-25B4B9E9C2A1
instance of	scholarly article
published in	wds:Q57276560-03772C6D-3F80-4206-AED1-98EBEBB6BA5A
published in	Journal of Chemical Physics
issue	wds:Q57276560-9CF1C194-EDA4-489D-BA9A-7112202049CD
volume	wds:Q57276560-28944671-0FB0-4F13-B592-853E770EF5A8
issue	24
volume	119
number of pages	wds:Q57276560-A84147C6-8724-44B6-952C-7E45F04C9B7F
number of pages	11 (xsd:decimal)
DOI	wds:Q57276560-C310E43F-59E4-482C-8C0D-F1F3B27E6C01
DOI	http://dx.doi.org/10.1063/1.1627296
DOI	10.1063/1.1627296
is about of	https://www.wikidata.org/wiki/Special:EntityData/Q57276560
is cites work of	An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping On the origins of approximations for stochastic chemical kinetics Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm. Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways. From in vivo to in silico biology and back The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade. The slow-scale stochastic simulation algorithm. Two classes of quasi-steady-state model reductions for stochastic kinetics. A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks Rule-based modeling of biochemical networks Accelerating the Gillespie τ-Leaping Method using graphics processing units A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics Efficient step size selection for the tau-leaping simulation method Discrete stochastic simulation methods for chemically reacting systems A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction Quantifying stochastic effects in biochemical reaction networks using partitioned leaping. Reduction and solution of the chemical master equation using time scale separation and finite state projection Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation. Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise Binomial leap methods for simulating stochastic chemical kinetics. Overcoming stiffness in stochastic simulation stemming from partial equilibrium: a multiscale Monte Carlo algorithm. Binomial distribution based tau-leap accelerated stochastic simulation. A general method for the computation of probabilities in systems of first order chemical reactions. An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine Adaptive explicit-implicit tau-leaping method with automatic tau selection A moment closure method for stochastic reaction networks. Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations Variable-free exploration of stochastic models: a gene regulatory network example. Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling. Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach A rigorous framework for multiscale simulation of stochastic cellular networks Multiscale spatial Monte Carlo simulations: multigriding, computational singular perturbation, and hierarchical stochastic closures. Computational systems biology and dose-response modeling in relation to new directions in toxicity testing. Efficient binomial leap method for simulating chemical kinetics. "All possible steps" approach to the accelerated use of Gillespie's algorithm. Simulating the evolution of soot mixing state with a particle‐resolved aerosol model Adaptive hybrid simulations for multiscale stochastic reaction networks Simulation of anaerobic digestion processes using stochastic algorithm Noise in biological circuits. Incorporating pushing in exclusion-process models of cell migration.

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