• RNAKinetics

  • Referenced in 4 articles [sw23818]
  • folding pathways, revealing important kinetic details that are not captured by the traditional structure prediction...
  • TChem

  • Referenced in 2 articles [sw12714]
  • chemistry and facilitates the analysis of detailed kinetic models. The toolkit provide capabilities for thermodynamic ... efficient time advancement and analysis of detailed kinetic models...
  • ReaDDy

  • Referenced in 3 articles [sw17865]
  • software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell ... contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits ... between small-scale but highly detailed molecular dynamics or Brownian dynamics ... simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design...
  • MPSalsa

  • Referenced in 24 articles [sw06960]
  • spatial dimensions when coupled with a detailed, fundamental chemistry model. The goal of our research ... equal emphasis on fluid flow and chemical kinetics modeling. In our research, we focus...
  • PoKiTT

  • Referenced in 1 article [sw17486]
  • data parallelism on heterogeneous architectures for detailed chemical kinetics, transport, and thermodynamics calculations. Simulating combustion...
  • OpenSMOKE++

  • Referenced in 0 articles [sw22162]
  • numerical modeling of reactive systems with detailed kinetic mechanisms. OpenSMOKE++ is a general framework ... numerical simulations of reacting systems with detailed kinetic mechanisms, including thousands of chemical species ... point of view. Since simulations involving large kinetic mechanisms are very time consuming, OpenSMOKE++ adopts ... present paper we give a detailed description of the framework features, the numerical models available...
  • EPISO

  • Referenced in 4 articles [sw02494]
  • velocity-pressure coupling is then given in detail, along with a similar technique ... turbulence model, in this case the turbulence kinetic energy and its dissipation rate. The EPISO...
  • Viriato

  • Referenced in 3 articles [sw22282]
  • appropriate limit) and (ii) the kinetic reduced MHD (KRMHD) equations (Schekochihin ... benchmarks and tests are presented, including a detailed analysis of 2D and 3D Orszag–Tang ... type decaying turbulence, both in fluid and kinetic regimes...
  • E-CELL

  • Referenced in 15 articles [sw07917]
  • simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models ... rules of the developed cell model with kinetic parameters can be obtained...
  • MetaCrop

  • Referenced in 1 article [sw23102]
  • different levels of detail from overview maps of primary metabolism to kinetic data of enzymes...
  • PARCS

  • Referenced in 5 articles [sw02913]
  • OpenMP to the U. S. NRC neutron kinetics code PARCS POSIX Threads and OpenMP were ... modules using POSIX threads and OpenMP. A detailed analysis of the cache misses was performed...
  • SPICES1

  • Referenced in 3 articles [sw01173]
  • SPICES1 - a smart-particle code for kinetic plasma simulation. SPICES1 (Smart Particle In Cell ElectroStatic ... required to use SPICES1 are given in details. Several test cases and paradigmatic applications...
  • ADMIT

  • Referenced in 1 article [sw14284]
  • Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding ... tutorial and in the examples. A detailed understanding of the underlying mathematical concepts...
  • CPMC-Lab

  • Referenced in 1 article [sw19934]
  • conditions. Importance sampling and all other algorithmic details of a total energy calculation are included ... dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps...
  • ABCRATE

  • Referenced in 2 articles [sw00011]
  • ABCRATE is a computer program that calculates rate...
  • LAPACK

  • Referenced in 1426 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • PARAMESH

  • Referenced in 79 articles [sw00677]
  • In this paper we describe a community toolkit...
  • RKC

  • Referenced in 91 articles [sw00808]
  • RKC: An explicit solver for parabolic PDEs. An...
  • SUNDIALS

  • Referenced in 152 articles [sw00927]
  • SUNDIALS was implemented with the goal of providing...
  • UMFPACK

  • Referenced in 252 articles [sw00989]
  • An ANSI C code for sparse LU factorization...