• # SGNS2

• Referenced in 2 articles [sw34966]
• SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. Motivation: Cell growth ... division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations ... them in silico, one needs to simulate these processes in great detail. Results: We present...
• # BIOCHAM

• Referenced in 45 articles [sw09927]
• modeling biochemical systems (compatible with SBML); several simulators (boolean, differential, stochastic), a temporal logic based ... developing/correcting/completing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints...
• # ntkfoam

• Referenced in 1 article [sw36388]
• OpenFOAM based neutron transport kinetics solver for nuclear reactor simulation. Due to the complexity ... namely ntkFoam, for the nuclear reactor kinetics simulation, from the governing equations to the detailed ... Euler implicit scheme, the transient kinetics problems are simulated. Numerical results show that the proposed ... ntkFoam can simulate the multi-group neutron transport kinetics problem accurately and flexibility, and both...
• # VAMPnets

• Referenced in 19 articles [sw32927]
• kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations ... Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension ... develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet...
• # kTAM

• Referenced in 1 article [sw22257]
• aTAM model has been extended to a kinetic counterpart (kTAM). Although there is a wide ... Patitz (2012) [22]), numerical simulations of the kinetic counterpart have been performed only ... advantages of this modelling framework for kinetic simulations of kTAM and the easy way such ... numerical simulations of kTAM, as well as comparison in between four different kinetic variant...
• # MIXKIP/RAPCAL

• Referenced in 1 article [sw40496]
• computational package for integrated simulations of large-scale atomic kinetics and radiation transport ... local thermodynamic equilibrium atomic kinetics and radiation transfer coupled simulations for high energy density plasmas ... This package includes different modules that allow simulations of non-equilibrium plasmas under different degrees ... plasma in the radiation dependent atomic kinetics simulations is also analyzed. Finally, this study...
• # SAAM II

• Referenced in 5 articles [sw27400]
• SAAM II: Simulation, analysis, and modeling software for tracer and pharmacokinetic studies. Kinetic analysis ... kinetic analysis. The purpose of this report is to describe one such software tool, Simulation ... models found in lipoprotein (apolipoprotein B [apoB] kinetics) and diabetes (glucose minimal model) research...
• # GEMS3K

• Referenced in 7 articles [sw19058]
• coupled simulation codes, Reactive mass transport (RMT) simulation is a powerful numerical tool to advance ... solubility, chemical kinetics, and RMT in general. Efficient RMT simulations can be based...
• # MESMER

• Referenced in 1 article [sw26915]
• open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where ... transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user...
• # DBSolve

• Referenced in 2 articles [sw09288]
• software package for kinetic modeling which allows dynamic visualization of simulation results. Background: Systems biology ... accordance to simulation results. This technique is applied to visualize both kinetic response ... kinetic model of the Krebs cycle. Conclusion: DBSolve Optimum is a user friendly simulation software ... kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results...
• # TOUGHREACT

• Referenced in 22 articles [sw07854]
• TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids ... fluids can occur under local equilibrium or kinetic rates. The gas phase can be chemically...
• # SIMKINE

• Referenced in 1 article [sw07174]
• user-friendly programme SIMKINE’ for simulation of kinetics involving complex reaction mechanisms A programme, SIMKINE ... rule and extrapolation to simulate complex mechanisms based on the kinetics of homogeneous chemical systems...
• # E-CELL

• Referenced in 23 articles [sw07917]
• reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly ... rules of the developed cell model with kinetic parameters can be obtained...
• # MLAB

• Referenced in 5 articles [sw06010]
• solving simulation and modeling problems such as chemical kinetics, pharmacological compartmental models, multiple site ligand...