Search Results for "diffusion"

ViennaSHE is a modern semiconductor device simulator for 1D, 2D and 3D device simulation. It relies on deterministic solutions of the Boltzmann Transport Equation using Spherical Harmonics Expansions.

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.

BioFVM is an open source diffusive transport solver for biological problems. It can solve for the diffusion of tens or hundreds of substrates on large 3-D domains. For simplicity, the code has minimal external dependencies. BioFVM was first published in: A. Ghaffarizadeh, S.H. Friedman, and P. Macklin. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics 32(8): 1156-8, 2016.

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

...Please cite the following papers if you use a curvature filter in your work. Traditional solvers, such as gradient descent or Euler Lagrange Euqation, start at the total energy and use diffusion scheme to carry out the minimization. When the initial condition is the original image, the data fitting energy always increases while the regularization energy always reduces during the optimization. Thus, regularization energy must be the dominant part since the total energy has to decrease. Therefore, Curvature filters focus on minimizing the regularization term, whose minimizers are already known. ...

This is a brownian motion simulator intended to model diffusion properties of different materials.

...Current version (r2766) includes * accurate propagation scheme * polarized synchrotron * free-free emission and absorption * new convection models * anisotropic diffusion * primary positrons * free-escape boundary conditions * new hadronic gamma-ray production models * new injection spectral breaks * upwards compatible with latest HEALPix * improved HEALPix skymap format * full reference output for a sample run * deuterium production by pp fusion * JF12 B-field * hadronic losses Full details in the Explanatory Supplement and README. ...

The project lives on GitHub - please see: https://github.com/DetlevCM/chemical-kinetics-solver

The OFR method is a type of steered molecular dynamics method for determining potentials of mean force (PMF) (Phys. Rev. E, 2011, 83: 021114) and local diffusion coefficients, D(z) (Phys. Rev. E, 2012, 86: 036707). OFR-AT is a fast and convenient program for analyzing large output data files from the OFR method, and returns the information necessary to quickly and easily calculate the PMF and D(z) in a spreadsheet. The software is described in detail in the following article: J. Comp. ...

...Motivated by several biological examples, we study the behavior of covalent modification networks when the activating component is localized to a planar membrane in either a random or clustered configuration. Reactions and diffusion are implemented on a three-dimensional lattice.

A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

This program simulates the performance of the supersonic continuous wave chemical laser by solving 2D-system of Navier-Stokes equations in slender-jet approximation that includes multi-component diffusion, non-equilibrium chemical reactions and radiation

FSEM is a set of freeFEM++ scripts and C++ code to solve the drift-diffusion (DD) semiconductor device equations by the finite element method (FEM). It was initially developed for the nonlinear study of semiconductors under high optical injection.

Qumax is an object-oriented Quantum Monte Carlo Program. It allows to perform calculations on atoms, molecules, solids, and provides different techniques to carry out calculations like Variational, Diffusion, Reptation, Stochastic Reconfiguration.