Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations

scientific article published on October 2012

Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1063/1.4758459
P932PMC publication ID3487926
P698PubMed publication ID23083152

P50authorKim T BlackwellQ41048257
P2093author name stringWonryull Koh
P2860cites workThe chemical basis of morphogenesisQ769913
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differencesQ21686228
Ionization Yield of Radiations. II. The Fluctuations of the Number of IonsQ21709246
Information Theory and Statistical MechanicsQ21709552
Noise in gene expression: origins, consequences, and controlQ24537307
The spread of Ras activity triggered by activation of a single dendritic spineQ24652704
Activation of CaMKII in single dendritic spines during long-term potentiationQ24658061
Microtubule self-organisation by reaction-diffusion processes causes collective transport and organisation of cellular particlesQ24794657
The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulationsQ27323091
Information Theory and Statistical Mechanics. IIQ27342071
Experimental Demonstration of Violations of the Second Law of Thermodynamics for Small Systems and Short Time ScalesQ27348541
PKA-I holoenzyme structure reveals a mechanism for cAMP-dependent activationQ27648438
Stochastic gene expression in a single cellQ28131784
Detailed simulations of cell biology with Smoldyn 2.1Q28473184
Biphasic synaptic Ca influx arising from compartmentalized electrical signals in dendritic spinesQ28476085
Subcellular dynamics of type II PKA in neuronsQ28581895
4 Maximum Entropy Production and Non-equilibrium Statistical MechanicsQ29027402
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many ChannelsQ29039318
The fluorescent toolbox for assessing protein location and functionQ29615075
Regulation of noise in the expression of a single geneQ29616626
Noise in eukaryotic gene expressionQ29617406
It's a noisy business! Genetic regulation at the nanomolar scaleQ33546905
FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.Q33641314
Dynamic spatial regulation in the bacterial cellQ33824724
Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiologyQ34105592
Molecular biological approaches to unravel adenylyl cyclase signaling and functionQ34263887
Stochastic reaction-diffusion kinetics in the microscopic limitQ34358936
Automatic generation of cellular reaction networks with Moleculizer 1.0.Q34382502
Efficient step size selection for the tau-leaping simulation methodQ34491625
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phasesQ34575248
An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leapingQ34948910
Dynamics of single-cell gene expressionQ35194039
cAMP activation of PKA defines an ancient signaling mechanism.Q35576088
Molecules into cells: specifying spatial architectureQ36337118
Stochastic simulation of chemical kineticsQ36622158
A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamicsQ36624025
Gonadotropin-releasing hormone-1 neuronal activity is independent of hyperpolarization-activated cyclic nucleotide-modulated channels but is sensitive to protein kinase a-dependent phosphorylationQ36755444
Protein kinase signaling in synaptic plasticity and memoryQ36820864
Regulating gene transcription in response to cyclic AMP elevationQ36997413
Fluctuation theoremsQ37130536
The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systemsQ37165376
The stochastic nature of biochemical networksQ37228971
Cyclic nucleotide-regulated cation channelsQ37340786
Fluctuations in nonequilibrium systemsQ37485852
Caught in the act: quantifying protein behaviour in living cellsQ37607827
Multi-scale modeling in biology: how to bridge the gaps between scales?Q37894287
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behaviorQ39216009
Teaching the principles of statistical dynamicsQ39745514
Measuring flux distributions for diffusion in the small-numbers limitQ40523772
A free-energy-based stochastic simulation of the Tar receptor complexQ40823091
Reaction-diffusion master equation, diffusion-limited reactions, and singular potentialsQ42251366
Maximum Caliber: a variational approach applied to two-state dynamicsQ43143040
Maximum caliber inference of nonequilibrium processesQ43479687
Efficient formulation of the stochastic simulation algorithm for chemically reacting systemsQ43939814
On the origins of approximations for stochastic chemical kineticsQ44135383
Dynamical fluctuations in biochemical reactions and cyclesQ44611374
Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithmQ47845317
Associative pairing enhances action potential back-propagation in radial oblique branches of CA1 pyramidal neurons.Q48288817
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coliQ48445530
Binomial leap methods for simulating stochastic chemical kineticsQ48513065
Pattern Formation inside Bacteria: Fluctuations due to the Low Copy Number of ProteinsQ50328692
Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.Q51542902
Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm.Q51715877
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions.Q51798914
Reactive boundary conditions for stochastic simulations of reaction-diffusion processes.Q51918379
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.Q51930664
Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.Q51962912
Mechanisms of calcium decay kinetics in hippocampal spines: role of spine calcium pumps and calcium diffusion through the spine neck in biochemical compartmentalization.Q52081862
Reaction-diffusion master equation: A comparison with microscopic simulations.Q52288534
A general method for numerically simulating the stochastic time evolution of coupled chemical reactionsQ55934780
Exact stochastic simulation of coupled chemical reactionsQ56536017
A rigorous derivation of the chemical master equationQ56536018
The chemical Langevin equationQ56536019
Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics SimulationsQ56563841
Approximate accelerated stochastic simulation of chemically reacting systemsQ56776006
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithmQ57022979
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping methodQ57276560
P433issue15
P407language of work or nameEnglishQ1860
P304page(s)154111
P577publication date2012-10-01
P1433published inJournal of Chemical PhysicsQ900472
P1476titleImproved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations
P478volume137

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cites work (P2860)
Q50598356Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.
Q39800646Asynchronous τ-leaping
Q38996023Fluctuating hydrodynamics of multi-species reactive mixtures
Q50750023Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

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