Polymer Simulation Images

Simulation I

In this animation a model protein consisting of 56 neutral hydrophobic monomers (gray spheres) and 44 charged hydrophilic monomers (green spheres) is simulated. As a first approximation, all 44 polymer charges (shown as red spheres) are assumed to have the same (nominal) negative sign and same magnitude. Positive and negative ions in solution are represented by blue and pink spheres. The density of ions is sustained by a grand canonical Monte Carlo, which causes ions to be added or removed from the simulation box based on the chemical potential. During the initial part of the animation only enough ions to neutralize the polymer are present and their number is kept fixed. In the second half of the animation the grand canonical routine is turned on and the density of ions equilibrates to a predetermined value. (14 Mb animated gif file)

Simulation II

This animation is similar to the one above, except that the density of ions is controlled by a grand canonical Monte Carlo during the entire animation. Halfway through the chemical potential is reduced by a factor of e², causing the ions to re-equilibriate at a approximately half of the initial density. (9 Mb animated gif file)