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Scientific Software

The Spherical HArmonic Parameterization Explorer (SHAPE) :

This small utility demonstrates the spherical harmonic parametrization. The user can create various shapes by changing spherical harmonic expansion coefficients directly. Please note that the program SHAPE uses the parametric implementation of the spherical harmonics, NOT the direct radial function expansions that physicists and chemists are familiar with from the solutions of the angular part of the Schroedinger equation of the hydrogen atom. This means that the three Cartesian coordinates are each expanded individually using spherical harmonics functions. (Please see: Khairy K., J. Howard, “Spherical Harmonics-Based Parametric Deconvolution of 3D Surface Images using Bending Energy Minimization” Medical Image Analysis, 12(2): 217-227, (2008) , and references therein for details.) This is why we have three sets of coefficients (the three tabs in the interface of SHAPE) that define the shape. Also SHAPE is limited to a maximum L order of 6. The Windows version also calculates on the fly some parameters: Area (starts with 1), Volume (bug alert! it doesn't update at the moment), Reduced volume: ratio of total volume to the volume of a sphere that has the same surface area (1 for sphere), Bending energy (assuming a bending modulus of 1), Total curvature, Wb: bending energy relative to that of the sphere. Shapes can be created with the program and saved as wavefront .obj format for compatibility with most CAD programs. The triangular mesh is made of 2500 vertices and 4996 faces..

The MacOS version of the program uses Cocoa and the visualization toolkit (VTK) for displaying shapes.

Download: ~1.4MB zip file (MacOSX) or 2.8MB rar file(win32) or 3.4MB zip file(win32)

Screenshot:

WinMOMD is an EPR-spectral simulation and analysis program. The simulation is based on the EPRLL programs of Freed and coworkers, which includes the slow motion regime of the spin-label and involves the solution of the stochastic Liouville equation.

Experimental spectra can be analyzed using either a secant Newton-type method (NL2SNO) of Dennis, Gay and Welsh, or the downhill simplex method of Nelder and Mead.

The program (currently the debug beta-version) runs under Windows (2000 or XP) and is written in C++ and FORTRAN. (Best run at screen resolution 1152 x 864).

Download: ~3.5MB zip file

Screenshot:

GAMMA is a C++ library written for simulation of Magnetic Resonance experiments.

PyGAMMA is an interactive, scriptable version of GAMMA that runs using a Python interpreter. It blends the object oriented scripting language Python with the GAMMA magnetic resonance simulation platform.

This project has recently been revived. For more information and downloads click here.