• # C-ImmSim

• Referenced in 5 articles [sw34210]
• Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based ... second level of description beyond the mesoscopic level of the inter-cellular interaction ... differentiation process in TH cells. Results: The simulator reproduces the hallmarks of an IgE-mediated ... example of how to combine the mesoscopic level description of immune cells with the microscopic...
• # ALLD

• Referenced in 2 articles [sw00030]
• ALLD simulation software implements a mesoscopic lattice method to model hydrophobic chromatographic systems and biomembranes ... described along with concepts for parallelization to simulate massive systems and large biomolecules. Extensions...
• # CERENA

• Referenced in 14 articles [sw19501]
• MATLAB-based toolbox for the simulation and analysis of chemical reaction networks using approximations ... stochastic biochemical reaction networks, focusing on mesoscopic and macroscopic descriptions, namely Reaction Rate Equation...
• # PyURDME

• Referenced in 2 articles [sw16723]
• meshes. The current core simulation algorithm is based on the mesoscopic reaction-diffusion master equation ... assembly, see http://fenicsproject.org/. The core simulation routines are implemented in C, and requires...
• # iNA

• Referenced in 4 articles [sw17973]
• Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter ... being in any one of the possible mesoscopic states; these equations are typically computationally intractable ... system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based ... expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have...
• # npFEM

• Referenced in 3 articles [sw39373]
• support): Bridging the computational gap between mesoscopic and continuum modeling of red blood cells ... present a computational framework for the simulation of blood flow with fully resolved red blood ... more commonly used mass-spring systems (mesoscopic modeling), such as an unconditional stability, versatile material...
• # MESOSCOP

• Referenced in 1 article [sw09084]
• flows with hydraulic jumps. For numerical simulation of three-dimensional atmospheric flows at micro ... finite-difference method has been developed (program MESOSCOP). In its non-hydrostatic variant it requires...
• # gLBM

• Referenced in 1 article [sw41223]
• algorithms for simulation. Unlike traditional formulations that simulate fluid dynamics on a macroscopic level with ... characterizes the problem on a mesoscopic level applied to a grid discretization. LBM solves...
• # MDMC2

• Referenced in 1 article [sw17668]
• Monte Carlo program devoted to Monte Carlo simulations of multiply charged clusters in the NVTNVT ... Both MCMC2 and MDMC2 codes employ a mesoscopic coarse-grained simplified representation of the clusters ... conservation, can be steadily checked during the simulation. The program also provides some statistical information...
• # ProtoMD

• Referenced in 0 articles [sw19021]
• algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture ... scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained ... toolkit integrates GROMACS wrapper’ to initiate MD simulations, and MDAnalysis’ to analyze and manipulate trajectory...