Smoldyn
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Cited in
(45)- Particle-based multiscale modeling of calcium puff dynamics
- Bayesian learning of effective chemical master equations in crowded intracellular conditions
- Accurate Particle-Based Reaction Algorithms for Fixed Timestep Simulators
- Multiscale modeling of diffusion in a crowded environment
- Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
- Multiscale Simulation of Stochastic Reaction-Diffusion Networks
- Diffusion-controlled reactions modeling in Geant4-DNA
- Multithreaded stochastic PDES for reactions and diffusions in neurons
- Sequestration of CaMKII in dendritic spines in silico
- Spatiotemporal maps of CaMKII in dendritic spines
- Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics
- Stochastic reaction-diffusion processes with embedded lower-dimensional structures
- Multiscale stochastic reaction-diffusion algorithms combining Markov chain models with stochastic partial differential equations
- STEPS
- MCELL
- URDME
- STOCHSIMGPU
- LBS
- PySB
- STEPS
- MOLNs
- PyURDME
- ReaDDy
- iNA
- MesoRD
- PARTRAC
- Eucalyptus
- GTW
- NeuroMorpho
- Parsec
- NFsim
- XTW
- Tyche
- BioSimulator.jl
- Cell++
- Smoluchowski Reaction Kinetics for Reactions of Any Order
- Executable biochemical space for specification and analysis of biochemical systems
- Simulation of stochastic diffusion via first exit times
- Comparative study of metaheuristics for the curve-fitting problem: modeling neurotransmitter diffusion and synaptic receptor activation
- Flexible single molecule simulation of reaction-diffusion processes
- rxncon
- Analysis and design of jump coefficients in discrete stochastic diffusion models
- Spatial stochastic intracellular kinetics: a review of modelling approaches
- Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs
- Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions
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