Ethan Liu (VI), Alex Wong (VI), Christian Zhou-Zheng (V), Katharine Luo (V), William Zhou-Zheng (IV), Ryan Hao (IV)
Project Summary
The Accelerated Molecular Dynamics Group aims to simulate physical systems by developing rapid molecular dynamics simulations using MATLAB programming. Our research looks into two different types of physical systems: dynamics of interacting particles (Interacting Particles subgroup), oscillatory dynamics involving spring networks (Spring Network subgroup). The interacting particles subgroup experiments with various numerical propagation methods to simulate both small-scale systems (e.g. particles in a box) and large-scale systems (e.g. planetary orbits). The Spring Network subgroup utilizes a simple propagator to simulate the behaviors of coupled, damped, and driven harmonic oscillators.
Project Goals
To construct a robust molecular dynamics scheme that can be performed on most personal computers and applied to physical systems in molecular biology, nanoscience, astronomy, fluid dynamics, quantum physics, and more.
Works Cited
Akimov, A., Prezhdo, O. The PYXAID Program for Non-Adiabatic Molecular Dynamics in Condensed Matter Systems. Journal of Chemical Theory and Computation 9(11), 4959-4972 (2013)
Feldmeier, H., Schnack, J. Molecular dynamics for fermions. Rev. Mod. Phys. 72(3). 655-688 (2000)
Hollingsworth, S, Dror, D. Molecular Dynamics Simulation for All. Neuron 99, 1129-1143 (2018).
Karplus, M., Petsko, G. Molecular dynamics simulations in biology. Nature 347, 631–639 (1990).
Van Gunsteren, W.F. and Berendsen, H.J.C. (1990), Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry. Angew. Chem. Int. Ed. Engl., 29: 992-1023
Faculty Advisor
Dr. Chester Chu
