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