• Kiva-2

  • Referenced in 65 articles [sw08987]
  • ease-of-use. The KIVA-2 equations and numerical solution procedures are very general ... flows. Arbitrary numbers of species and chemical reactions are allowed. A stochastic particle method ... program, we describe in detail the equations solved, the numerical solution procedure, and the structure...
  • CERENA

  • Referenced in 13 articles [sw19501]
  • analysis of chemical reaction networks using approximations of the Chemical Master Equation solution statistics. CERENA ... methods for the analysis of stochastic biochemical reaction networks, focusing on mesoscopic and macroscopic descriptions...
  • Uintah

  • Referenced in 19 articles [sw12921]
  • complex chemical and physical reactions. These reactions are modeled by solving partial differential equations...
  • MesoRD

  • Referenced in 30 articles [sw18202]
  • tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation ... Markov process corresponding to the reaction-diffusion master equation. Availability: MesoRD is free software, written...
  • OPPDIF

  • Referenced in 6 articles [sw15840]
  • form of the discretized equations. The CHEMKIN package evaluates chemical reaction rates and thermodynamic...
  • SIDAC

  • Referenced in 1 article [sw09278]
  • mathematical and chemical objects like differential equations, chemical reactions and functions. The system was developed...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • numerically integrating the differential equations described implicitly in these reaction rules. The user can observe ... concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software...
  • PREMIX

  • Referenced in 34 articles [sw27815]
  • molecular transport. After stating the appropriate governing equations and boundary conditions, we discuss the finite ... conjunction with preprocessors for the chemical reaction mechanism and the transport properties. Transport property formulations...
  • SENKIN

  • Referenced in 20 articles [sw12845]
  • elementary chemical reactions, and performs kinetic sensitivity analysis with respect to the reaction rates ... solve both the nonlinear ordinary differential equations that describe the temperature and species mass fractions ... linear differential equations that describe the first-order sensitivity coefficients of temperature and species composition ... reaction rates. The program runs in conjunction with the CHEMKIN package, which handles the chemical...
  • SOSlib

  • Referenced in 4 articles [sw29331]
  • system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded...
  • HOLOMAC

  • Referenced in 6 articles [sw18067]
  • equations relies on an operating-split strategy, where chemical reactions are solved implicitly with ... employed to solve a variable-coefficient Poisson equation. The numerical implementation takes advantage ... reacting flows to understand complex turbulent and chemical phenomena in flames...
  • Larkin

  • Referenced in 4 articles [sw36286]
  • Systems Arising in Chemical Reaction KINetics. Chemical reaction kinetics is one of the most important ... ordinary differential equations occur. In fact, even the term ‘stiff’ originated from chemical kinetics...
  • MUSCOD-II

  • Referenced in 19 articles [sw13053]
  • differential equations (ODE) or by differential-algebraic equations (DAE) of index one. MUSCOD ... problems, in particular in the field of chemical engineering. The software has the capability ... several coupled process stages, e.g., a batch reaction step followed by a batch separation step...
  • Dizzy

  • Referenced in 18 articles [sw35541]
  • stochastic and deterministic simulation of chemical reactions. Developed by the Bolouri institute in Seattle, this ... models using both ordinary and stochastic differential equation solvers. In addition, Dizzy allows users...
  • sbioPN

  • Referenced in 5 articles [sw11725]
  • chemical reactions are defined. For deterministic solutions, sbioPN creates the associated system of differential equations...
  • CHEMEQ2

  • Referenced in 4 articles [sw18289]
  • Stiff Ordinary Differential Equations of Chemical Kinetics. This report describes and documents the subroutine CHEMEQ2 ... integrate stiff ordinary differential equations arising from reaction kinetics. This is a second generation improvement...
  • KinFitSim

  • Referenced in 6 articles [sw09290]
  • chemical or biochemical reactions given the information about the stoichiometry of the reaction mechanism, kinetics ... each reaction and initial concentrations of all species. Simulated data may be plotted ... numerical solution of ordinary differential equation (ODE) systems and fitting, reducing the need for users...
  • ABC

  • Referenced in 4 articles [sw09004]
  • reactive scattering program for atom-diatom chemical reactions that we have written during the past ... hyperspherical coordinate method to solve the Schrödinger equation for the motion of the three nuclei...
  • ERODE

  • Referenced in 5 articles [sw20210]
  • exact reduction of systems of ordinary differential equations (ODEs). The tool supports two recently introduced ... degree at most two, covering elementary chemical reaction networks (CRNs) and continuous time Markov chains...
  • RETRASO

  • Referenced in 2 articles [sw37010]
  • exchange, precipitation and dissolution of minerals). Chemical reactions can be assumed to follow either ... direct substitution approach. That means that all equations are solved simultaneously by applying Newton-Raphson...