• APBS

  • Referenced in 92 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media...
  • GAMESS

  • Referenced in 40 articles [sw03002]
  • discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic...
  • RIPPLE

  • Referenced in 57 articles [sw30642]
  • volume force derived from the continuum surface force ( CSF) model. A two-step projection method...
  • PDB2PQR

  • Referenced in 35 articles [sw13087]
  • setup of Poisson–Boltzmann electrostatics calculations. Continuum solvation models, such as Poisson–Boltzmann and Generalized ... radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing...
  • CompuCell3D

  • Referenced in 23 articles [sw34248]
  • simulations using the Glazier-Graner-Hogeweg (GGH) model, a cell-oriented framework designed to simulate ... simulation, based on the hybrid (continuum-discrete) model of Picioreanu, van Loosdrecht, and Heijnen...
  • PERMIX

  • Referenced in 24 articles [sw09519]
  • source software framework called PERMIX for multiscale modeling and simulation of fracture in solids ... GMSH. Fracture on the continuum level is modeled by the extended finite element method (XFEM ... concurrent multiscale methods for fracture, coupling two continuum domains or atomistic domains to continuum domains ... through several simulations including a 3D crack modeling in clay nanocomposites, a semi-concurrent...
  • Y-Geo

  • Referenced in 12 articles [sw30877]
  • technique that combines the advantages of continuum-based modeling approaches and discrete element methods ... offers the ability to explicitly model the transition from continuum to discontinuous behavior by fracture ... shear strength criterion, (4) a dissipative impact model, (5) an in situ stress initialization routine...
  • MFIX-DEM

  • Referenced in 10 articles [sw18199]
  • lead to better closures for the continuum modeling (or traditionally referred to as two fluid ... model) of gas–solids flows. In this paper, a series of verification cases is employed ... testing any new developments that couple continuum and discrete formulations for gas–solids flows...
  • ARVO

  • Referenced in 14 articles [sw00049]
  • computing the percolation probability of continuum percolation models...
  • FLAG

  • Referenced in 10 articles [sw09041]
  • away from the material. Modeling such phenomena in a continuum hydrodynamics code challenges the assumptions ... compatible with continuum mechanics. Earlier work documents an initial effort in modeling ejecta ... framework. To model ejecta in FLAG, a hybrid particle-continuum representation was defined that allows ... coupling with continuum materials on large (bulk) scales. Numerical models were developed and implemented...
  • SDPBS

  • Referenced in 7 articles [sw17208]
  • important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently...
  • TWINLAW

  • Referenced in 5 articles [sw35042]
  • magnitude slower than a conventional continuum model with isotropic hardening. TWINLAW reproduces...
  • PyGBe

  • Referenced in 5 articles [sw17642]
  • molecular-electrostatics calculations in a continuum model. It computes solvation energies for proteins modeled with...
  • FEniCS-HPC

  • Referenced in 5 articles [sw29445]
  • Unicorn, the Unified Continuum solver for continuum modeling based on the Direct FEM Simulation...
  • VAMUCH

  • Referenced in 15 articles [sw13343]
  • method is used to develop a micromechanics model for predicting the effective properties and local ... enthalpy of the heterogeneous continuum, we formulate the micromechanics model as a constrained minimization problem...
  • Flow123d

  • Referenced in 4 articles [sw13697]
  • different dimensions. Therefore, we can combine continuum models and discrete fracture network models. Current version...
  • Yifei2020Dimensionality

  • Referenced in 2 articles [sw41680]
  • conditions. A key feature of the discrete model is that crowding effects are introduced ... birth/death events. The continuum limit description of the discrete model is a nonlinear reaction-diffusion ... effect. Using both the discrete and continuum modelling tools, we explore the complicated relationship between ... required to solve the discrete and continuum models used in this work are available...
  • AQUASOL

  • Referenced in 3 articles [sw17113]
  • solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity...
  • npFEM

  • Referenced in 3 articles [sw39373]
  • computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood...
  • BioShape

  • Referenced in 7 articles [sw08522]
  • Consequently, several approaches have been defined to model such a process at different spatial ... levels and, in particular, in terms of continuum properties, abstracting in this way from ... information is available to validate such models separately, more work is needed to integrate ... simulation allows for tuning continuum-based tissutal and cellular models, as well as for better...