Simple Hydrophobic/Hydrophilic Protein Folding Model ` - Jun 28, 2014

The Simple Hydrophobic/Hydrophilic Protein Folding Model implements a 2-Dimensional hydrophobic/hydrophilic (HP) folding protein  to test the energetics of protein folding, the change in size of a protein relative to energy, and the computation time for complex protein problems. A Metropolis Monte-Carlo algorithm is used to determine if randomly guided movements are carried out by monomers (non-specific amino acids) within the polymer (protein tertiary structure).

Graphs and Tracks Model ` - May 30, 2012

The Graphs and Tracks Model implements the classic simulation by David Trowbridge.  The EJS version allows instructors to create custom configurations for teaching.  Instructors set the heights of the track segments and the model displays the position-space particle motion as well as position and velocity graphs and tables.  The customized simulation is then saved with associated curricular as a new jar file that can be redistributed.

Confined Hard Disk Two Piston System Model ` - Nov 3, 2011

The Confined Hard Disk Two Piston System simulates a constant-energy two-dimensional system of unit mass particles confined by two frictionless pistons of equal mass M.   This computer model was featured on the cover of the American Journal of Physics.

STP Percolation Program ` - Mar 31, 2009

The STP Percolation program generates occupied lattice sites for a given probability and determines the clusters of occupied sites. This program demonstrates properties of percolation, especially near the geometric phase transition, and is part of a group of  simulations for Statistical and Thermal Physics.

Orbit Program ` - Jul 6, 2008

The Orbit program displays the dynamics of multiple massive objects interacting gravitationally.  The default scenario shows the figure-eight orbit of three particles first discovered by Montgomery.   Additional particles and their initial positions and velocities can be specified.

Polarizer Program ` - Jul 6, 2008

The Polarizer program displays the effect of a plane polarizer on an incident electromagnetic wave.   The default electromagnetic wave is plane polarized but this polarization can be changed using the input fields.  The slider can be used to rotate the polarizer to change its orientation.

QM Wigner Program ` - May 1, 2007

The QM Wigner program displays the position-space wave function and the associated quasi phase space probability distribution using the Wigner function.