• OpenFOAM

  • Referenced in 552 articles [sw04317]
  • fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics...
  • CRNreals

  • Referenced in 5 articles [sw13616]
  • identifiability analysis of biochemical reaction networks. Chemical reaction network theory is widely used in modeling ... biologically and chemically important qualitative dynamical features, chemical reaction networks (CRNs) have attracted significant attention...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations ... proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed...
  • StochDynTools

  • Referenced in 3 articles [sw14944]
  • compute approximate moment dynamics for a stochastic network of chemical reactions...
  • MAZE

  • Referenced in 1 article [sw40351]
  • Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation...
  • CRNSimulator

  • Referenced in 3 articles [sw33636]
  • foundation for syntactic manipulation of chemical reaction networks as Mathematica expressions. It allows mixing ... dynamics, and provides a simple way to simulate experiments in which a sequence of chemical ... well-suited for engineered chemical systems, in which chemical reaction networks can be used...
  • ChemPAK

  • Referenced in 3 articles [sw18708]
  • dynamics reactor. he ChemPAK program package for solving direct problems of chemical ... kinetics with an arbitrary number of chemical reactions is suggested. The package contains an expandable ... hydrocarbon’s pyrolysis in gas-dynamics reactor with emission has been numerically simulated using...
  • ppsim

  • Referenced in 2 articles [sw38637]
  • studied subclass of chemical reaction networks (CRNs) in which all reactions have two reactants ... products. Each step in the dynamics involves picking a uniform random pair from a population ... Jupyter notebooks, allowing robust visualization of time dynamics such as histogram plots at time snapshots ... product) or unimolecular (1 reactant, 1 product) reactions, with arbitrary rate constants, and compiles...
  • Stiff-PINN

  • Referenced in 1 article [sw42094]
  • stiff chemical kinetics shall open the possibility of applying PINN to various reaction-diffusion systems ... involving stiff dynamics...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm ... drawn from several distributions and the reaction rates from complex functions or from physical parameters ... model specific GRNs and systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy...
  • ERODE

  • Referenced in 6 articles [sw20210]
  • obtained; each aggregate ODE gives the cumulative dynamics of the sum of the original variables ... degree at most two, covering elementary chemical reaction networks (CRNs) and continuous time Markov chains...
  • PORFLOW

  • Referenced in 2 articles [sw08691]
  • variably saturated, porous or fractured media with dynamic phase change. The porous/fractured media ... pumping wells) may be present and, chemical reactions or radioactive decay may take place...
  • LNetReduce

  • Referenced in 1 article [sw42168]
  • tool that simplifies linear dynamic networks. Dynamic networks are represented as digraphs labeled by integer ... models describe deterministic or stochastic monomolecular chemical reaction networks, but also random walks on weighted ... rewriting rules and reproduces the full network dynamics with good approximation at all timescales...
  • SOSlib

  • Referenced in 5 articles [sw29331]
  • differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup ... inspection of a model’s structure and dynamics. All functionalities are accessible directly...
  • GeoSysBRNS

  • Referenced in 5 articles [sw13424]
  • reaction network simulator BRNS) allows for the integrated simulation of groundwater flow, transport of chemically ... reactive species, and (bio-) chemical processes transforming them in up to three spatial dimensions. Flexibility ... species in GeoSysBRNS can refer to actual chemical compounds, or to pseudo-species. These ... isotopologically heavy fraction of an organic compound. Chemical and biochemical processes can be kinetically controlled...
  • BRTSim

  • Referenced in 2 articles [sw37291]
  • computational solver for hydrological, biogeochemical, and ecosystem dynamics. This paper introduces the recent release v3.1a ... liquid, gas and heat flow solver for reaction-advection-dispersion processes in porous ... platform, the user can define (1) arbitrary chemical and biological ... species; (2) arbitrary chemical and biological reactions; (3) arbitrary equilibrium reactions; and (4) combine solvers...
  • Facile

  • Referenced in 1 article [sw28767]
  • even the existence of interactions between some chemical species are unknown. It is therefore important ... removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics...
  • REANN

  • Referenced in 1 article [sw40919]
  • LAMMPs is provided for large scale molecular dynamics simulations. We hope that this open-source ... potential energy surfaces and quantum-chemical properties of molecules, reactions, and materials...
  • SGNS2

  • Referenced in 2 articles [sw34966]
  • compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. Motivation: Cell growth and division affect ... present SGNS2, a simulator of chemical reaction systems according to the Stochastic Simulation Algorithm with...
  • PhysNet

  • Referenced in 2 articles [sw40931]
  • performance of ML models for describing chemical reactions, long-range interactions, and condensed phase systems ... RMSD = 0.21 Å). By running unbiased molecular dynamics (MD) simulations of Ala10 on the PhysNet...