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//  Title

Interactive Simulation of Anisotropic Diffusion of Water

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// Summary

This project simulates water molecules whose
random motion is partially constrained in one direction.

Molecules are treated as points that have
a certain potential that governs their motion.

The directional constraint is established by stationary
points distributed along parallel lines.


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// Computational simulation

I use the "moldy" molecular dynamics simulation written
by Keith  Refson.

  http://www.earth.ox.ac.uk/~keithr/moldy.html

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// Static scene design

The static scene includes stationary spheres spaced closely
along parallel lines. These obstacles limit the random
motion of molecules.


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// Dynamic scene

The simulation consists of random motion of water molecules
partially constrained by the stationary guide lines.

A set of vectors outside the scene is constantly updated.
The vectors point in many different directions in R3.
The length of a vector v_k is determined by the average velocity
of the water molecules in direction v_k.

We expect to see the anisotropy revealed by the distribution
of lengths of these vectors v_k, forming an ellipsoidal shape.



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// 3D interaction

The user can specify the temperature of the water using
a 1-dimensional dragger with 2D text.

The user can mark a molecule by picking it and using 
the color editor. Colors can be copied and pasted.

The user can set the spacing of the parallel lines, the
spacing of the stationary molecules, and the size of the
stationary molecules.



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// 2D interaction

The File menu allows the option to Open and Save the
state of a simulation.



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// Documentation

A Web area documenting the project will be placed within
my course Web area.

The project Web area includes

  a description of diffusion-weighted MRI

  screen shots and animated gifs of my interactive simulation

  a description of how to use the 3D and 2D interactions,
  with figures to illustrate their use

  a link to my source code tarball
  
  installation instructions

  this project description