Modeling Calmodulin

One of our projects in BMI 214 (Representational Algorithms for Molecular Biology) taught by Dr. Russ Altman, was to create a molecular dynamics simulation of a protein. Molecular Dynamics is using computers to simulate the interaction of atoms and molecules for a period of time under known laws of physics. I represented a fragment of the protein calmodulin by simulating the interactions of its component atoms (each atom within each amino acid). This entails modeling (simulating) how each atom's mass, velocity, energy, and forces change over time, and calculating the effect of the previous moment in time on the subsequent moment.