Search Results for "chemical reaction"
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Showing 26 open source projects for "chemical reaction"
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ChemCrow
Chemcrow
ChemCrow is an AI-powered framework designed to assist in chemical research and discovery. It integrates AI models with chemical knowledge bases to provide intelligent recommendations for synthesis planning, reaction prediction, and material discovery. This tool helps automate and accelerate research in computational chemistry and drug development. -
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Catalyst.jl
Chemical reaction network and systems biology interface
Catalyst.jl is a symbolic modeling package for analysis and high-performance simulation of chemical reaction networks. Catalyst defines symbolic ReactionSystems, which can be created programmatically or easily specified using Catalyst's domain-specific language (DSL). Leveraging ModelingToolkit and Symbolics.jl, Catalyst enables large-scale simulations through auto-vectorization and parallelism. Symbolic ReactionSystems can be used to generate ModelingToolkit-based models, allowing the easy simulation and parameter estimation of mass action ODE models, Chemical Langevin SDE models, stochastic chemical kinetics jump process models, and more. ... -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations", J. ... -
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ChemCalc
Easily set up simulations or estimate needed amounts
...Examples of use: - Setting up a simulation by obtaining the mole fractions of each molecular entity - Anticipating the amounts of raw materials required to carry out a multi-step preparation for a chemical reaction -
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Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.
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FEATool Multiphysics - FEA & CFD Toolbox
FEATool Multiphysics is an easy-to-use FEA and CFD Simulation Toolbox
FEATool Multiphysics (https://www.featool.com) is a fully integrated toolbox for computer aided engineering CAE, finite element analysis & fluid dynamics simulations. With a very easy-to-use GUI, anyone is now able to quickly set up and perform large scale dynamical and complex engineering physics simulations, with coupled fluid flow, heat transfer, structural mechanics, chemical transport, and electromagnetics effects, without having to learn complex programming. In addition to... -
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CRP - Chemical Reaction Prediction
Predicting Organic Reactions using Neural Networks.
The intend is to solve the forward-reaction prediction problem, where the reactants are known and the interest is in generating the reaction products using Deep learning. This Graphical User Interface takes simplified molecular-input line-entry system (SMILES) as an input and generates the product SMILE & molecule. Beam search is used in Version 2, to generate top 5 predictions. Maximum input length for the model is 15 (excluding spaces). -
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MoCalc2012
GUI for MOPAC, DFTB+, GAMESS, Firefly, NWChem, ORCA and PSI4
MoCalc2012 is a simple, efficient Graphical User Interface for MOPAC, DFTB+, GAMESS(US), Firefly, NWChem, ORCA and PSI4. -
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Rhea is a reaction database, where all reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest). Rhea provides built-in validations that ensure both mass and charge balance of the reactions.
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Continuous time Markov chain (CTMC) can be used to describe describe the number of molecules and the number of reactions at any given time in a chemical reaction system. Gillespie algorithm is an important stochastic simulation algorithm, used to simulate each reaction track events of continuous time Markov chain in the number of collision frequency and collision time, but the computational cost is inevitably. In this project, Gillespie’s algorithm with rejection sampling introduces the rejection sampling theory to reduce the simulation times, and then speeds up the simulation efficiency.
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...Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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ddtFoam
OpenFOAM solver to simulate the deflagration-to-detonation transition
This solver represents an addition to the open-source CFD package OpenFOAM. The solver is used to simulate the deflagration-to-detonation transition in hydrogen-air mixtures. Prominent features are described below. Additional description is available in the pdf file included. For a more detailed description download Florian Ettner's thesis (in German) from http://www.td.mw.tum.de/tum-td/de/forschung/dissertationen/download/I2013/Ettne13.pdf [8.6 MB] A shorter description (in... -
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ForStoch
Fortran Stochastic Simulator for Chemical Kinetics
ForStoch is a FORTRAN software suite for Stochastic Simulation of Checimal Kinetics. The stochastic simulation algorithm (SSA), proposed by Gillespie, is a cardinal simulation method for the chemical kinetics. Because the SSA simulates every reaction event, the amount of the computational time is huge when models have many reaction channels and species.This drawback motivates many attempts to improve the efficiency with the accuracy.The ForStoch includes orignial Gillespie SSA and other approximation algorithms. You can run very simply the algorithms with several test case systems. ... -
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Chemical Reaction
Balance chemical reaction and compute material balance
This Python program is used to balance a chemical reaction and to compute the material balance. Furthermore, it's able to check molecules and to write the condensed strutural formula from the name of an organic molecule. (Those both functionalities are still limited.) -
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Acuchem: A Computer Program for Modeling Complex Chemical Reaction Systems by Walter Braun and John T. Herron This project creates a Java user interface to create and convert input/output files from the Acuchem program.
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The DetStoch package offers the user two different methods to compute chemical reactions: Deterministic and Stochastic approaches. It allows the user to play with an intuitive GUI framework and compute the evolution rates of the chemical reactions with the different methods available. The results are displayed in graphical plots of the species concentration over the time. The package is designed to solve any of the following reactions by either one of the two approaches mentioned: Synthesis-Decompostion Reaction Chain Reaction Nuclear Chemical Reaction Lodka Model Brusselator Model Furthermore, the Stochastic approach can be computed by several stochastic simulation algorithms. ...
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SPSens
Stochastic parameter sensitivity analysis for chemical networks
SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. ... -
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Easily find and extract specific chemical reactions from the BioModels database.
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A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.
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CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.
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DRCS (Dimensionless Reaction Coordinate Software) calculates a dimensionless reaction coordinate for chemical reactions that can be used to classify transition states (and other geometries along a reaction path) as either early or late.
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ReactionLab is a software package aimed for a unified computer environment to kinetic modeling of chemical reaction systems. The present implementation is founded on Matlab and Java-Swing GUI, with an interface to legacy C (and Fortran) codes.
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CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.
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Trelis is a graphical Monte Carlo simulation tool for modeling the time evolution of chemical reaction systems involving small numbers of reactant molecules, such as occur in subcellular biological processes like genetic regulatory networks.
