Molecular Dynamics Simulation of Lennard-Jones Potential, Hans Watanabe, UG '26 (3993975)

I have been coding this Java program for the past month with the guidance of Yury Polyachenko, a PhD student at the Jacobs lab specializing in molecular dynamics. The program simulates a box of atoms interacting with each other in 3D space via the Lennard-Jones potential. By implementing periodic boundary conditions, this small box acts as an accurate representation of the dynamics of a large/infinite volume of particles. With this simulation, the movement of individual particles or a system of particles as a whole can be studied at different temperatures, different particle densities/pressure, and different particle mass. The simulation's 2D display shows two dimensions (width and height) pretty clearly. However, the third dimension (depth) is represented using a color gradient, with particles close to the screen being colored red, further away particles being green, and the furthest particles being blue. A 3D display is something I plan to work on later. I also have plans to port this program to C/C++. Although this program is very STEM-oriented, I also consider it to be just as much a creative project as it is a science/coding project. To me, coding and the presentation of science is an important form of artistic creativity. Whether I am perfecting a drawing or solving a coding problem, it feels the same. Plus, the many moving colors in the display is very mesmerizing and is just fun to look at.