• MesoRD

  • Referenced in 32 articles [sw18202]
  • Stochastic reaction-diffusion simulation with MesoRD. Summary: MesoRD is a tool for stochastic simulation ... chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method ... exact method to simulate the Markov process corresponding to the reaction-diffusion master equation. Availability...
  • PRED_PREY

  • Referenced in 86 articles [sw12310]
  • simulating the dynamics of predator-prey interactions modelled by nonlinear reaction-diffusion systems. The collection ... simulating the dynamics of predator-prey interactions modelled by a nonlinear reaction-diffusion system. Unlike...
  • Camino

  • Referenced in 20 articles [sw15543]
  • edge techniques, such as Monte-Carlo diffusion simulation, multi-fibre and HARDI reconstruction techniques, multi...
  • ddfermi

  • Referenced in 13 articles [sw21481]
  • ddfermi -- a drift-diffusion simulation tool. ddfermi is an open-source software prototype which simulates...
  • Smoldyn

  • Referenced in 23 articles [sw23962]
  • over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces ... accurate and faster than other particle-based simulators. Smoldyn’s unique features include: a ”virtual...
  • STEPS

  • Referenced in 18 articles [sw17866]
  • STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. We describe ... program STEPS. STEPS is a simulation ... platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional ... modelers in how they could control the simulation and becoming increasingly complex as new features...
  • DICTRA

  • Referenced in 9 articles [sw27312]
  • DICTRA, a tool for simulation of diffusional transformations in alloys. In the present paper ... general survey of the diffusion-controlled transformations (DICTRA) software is given ... DICTRA is an engineering tool for diffusion simulations in multicomponent alloys. The simulations are based ... multicomponent diffusion and thermodynamic data, both obtained by analyzing and assessing experimental information. This allows...
  • Sim.DiffProc

  • Referenced in 9 articles [sw17081]
  • package Sim.DiffProc. Simulation of Diffusion Processes. Provides the functions for simulating and modeling of stochastic...
  • DifferentialEquations.jl

  • Referenced in 58 articles [sw23910]
  • discrete equations (function maps, discrete stochastic (Gillespie/Markov) simulations), ordinary differential equations, stochastic differential equations, algebraic ... delay differential equations, hybrid differential equations, jump diffusions, and (stochastic) partial differential equations. Through extensive...
  • DiffProc

  • Referenced in 7 articles [sw14956]
  • Sim.DiffProc: Simulation of Diffusion Processes. Provides the functions for simulation and modeling of stochastic differential...
  • EpiSimdemics

  • Referenced in 7 articles [sw36952]
  • certain class of stochastic reaction-diffusion processes. Straightforward simulations of such process do not scale...
  • SDA

  • Referenced in 4 articles [sw08089]
  • Simulation of the diffusional association of barnase and barstar. The rate of protein association places ... which, under certain circumstances, can be diffusion-controlled. Simulations of model proteins show that diffusion ... protein association explained by Brownian dynamics computer simulations. Proc. Natl. Acad. Sci. U.S.A...
  • URDME

  • Referenced in 26 articles [sw10400]
  • general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes ... general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes ... interactive environment for model construction. The core simulation routines are logically separated from the model...
  • GFET

  • Referenced in 4 articles [sw35926]
  • full coupled drift-diffusion-Poisson simulation of a GFET. A graphene field effect transistor (GFET ... graphene, is simulated including a full 2D Poisson equation and a drift-diffusion model with ... agreement with experimental data and other simulations known in the literature and based on compact...
  • KFAS

  • Referenced in 16 articles [sw14662]
  • forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization...
  • Phantomas

  • Referenced in 2 articles [sw23302]
  • Phantomas: a flexible software library to simulate diffusion MR phantoms. We introduce Phantomαs, an open...
  • UHBD

  • Referenced in 8 articles [sw08088]
  • Electrostatics and diffusion of molecules in solution – simulations with the University-of-Houston Brownian dynamics...
  • CA3D

  • Referenced in 4 articles [sw03304]
  • Monte Carlo code to simulate 3D buffered diffusion of ions in sub-membrane domains...
  • pydiffusion

  • Referenced in 1 article [sw28356]
  • pydiffusion: A Python Library for Diffusion Simulation and Data Analysis. pydiffusion is a free ... open-source Python library designed to solve diffusion problems for both single-phase and multi ... features of pydiffusion include fast simulation of multi-phase diffusion and extraction of diffusion coefficients ... using forward simulation analysis. pydiffusion also provides various mathematical models for diffusion profile smoothing, diffusion...
  • COUPLEX

  • Referenced in 32 articles [sw07861]
  • first test case is related to simulations based on a simplified 2D far-field model ... management. It leads to a classical convection diffusion type problem, but with highly variable parameters...