My name is Alex Olinger, and I had the pleasure of working with Dr. Amit Chakrabarti's group during this summer at the K-State physics REU.  My project was to simulate and study the aggregation of globular protein monomers in solution.  The codes I used were written in Fortran90. The particles in my simulation are on the nanoscale, having a diameter of 3-4 nm, and were under a random force which is described through Brownian Dynamics.  In my simulation, the proteins are represented by spheres with a uniform surface charge distribution.  Since there is a uniform charge distribution each monomer has a fluctuating dipole moment which causes an attractive Van der Waals force between the monomers. This attractive potential is represented by a modified Lennard-Jones potential for hard spheres.  The charge of the monomers also creates a repulsive Coulombic force.  However, by effectively representing salt in the solution containing the monomers, I can screen the Coulombic potential between the monomers by increasing the concentration of salt in solution which affects the number of negatively charged ions in solution. The negatively charged ions are attracted to the proteins, resulting in the creation of a neutral barrier around the protein.  See figure (1).  I used the Yukawa potential for hard spheres to model this potential.  I can also effect the aggregation of the proteins by changing the volume fraction (comparison of the number of particles and the size of my system) of my system and the temperature of my system.  In my simulations, the number of particles and the temperature of the system remain constant.  The condition of constant temperature was used due to the relatively constant temperature of the human body. 

Figure 1