APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
Range Software is software for finite element analysis (FEA) in engineering simulations. Its main features are support for Computational Fluid Dynamics (CFD), heat transfer and radiation, linear stress-strain, electro-statics, acoustics, ground water flow, shape optimization, 3D mesh generation, an intuitive GUI, and import and export functionality. The Range Software package contains several tools which helps the user to setup, solve, and analyze the engineering problem.
gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.
TheCurves is an application that plots a parameterized family of curves based on algebraic formulas specified by the user. It is meant as an educational tool for mathematics, physics, and engineering. When the program is run as an applet in a Web page, the plot parameters and formulas are configurable by HTML and dynamically scriptable, so that the applet can be initialized to present a specific plot when the page is opened or to change plots when the user clicks on a control in the Web page.
bcr harms takes a model of the quantum harmonic oscillator and adapts it as a soft synth. It lets you hear and see how the oscillator wave functions evolve in real-time as you modify amplitudes and other parameters. The user interface is based on and integrates with the BCR2000 MIDI controller, but the application can be used without a controller.
Code_Aster offers a full range of multi-physical analysis and modelling methods that go well beyond the standard functions of software for computational thermomechanics: static and dynamic mechanics, linear or not, modal analysis, harmonic and random response, seismic analysis, acoustics, thermics, fracture, damage and fatigue, multiphysics, drying and hydratation, metallurgy analysis ,soil-structure, fluid-structure interactions, geometric and material non linearities, and contact and friction. It has a wide range of material properties (95 constitutive laws): porous media, geomaterials, damage, elastoplasticity, elastoviscoplasticity, etc., a wide range of finite elements (395), and a wide range of loadings.