Educational Links

An Introduction to Graph Analysis of Chemistry Simulation Data

Abstract: This tutorial covers the conversion of chemical data in Molecular Dynamics simulations into graphs for use in data analysis.  For this tutorial, hydrogen bonding is examined through edge distribution analysis of a graph representation of a liquid water system.  The test system was drawn from a LAMMPS MD simulation of equilibrated liquid water consisting of 128 water molecules contained

within a periodic box of approximately 16 3.  A small portion of this data, 11 timesteps, was pulled for the analysis.  Using this data, we instruct on how to perform the following tasks.

  • Selectively load portions potentially large MD data sets using PANDAS
  • Construct graph of chemical systems using NetworkX v2.5
  • Perform computationally efficient graph edge creation based on pair-pair distance criteria in periodic systems
  • Visualize chemical systems in 3D coordinate space and 2D graph space
  • Determine edge distribution from graphs of the sample water system
  • Use random sampling to determine edge distributions for efficient analysis of large data sets

About the Author: Daniel J. Pope is a Ph.D. student in physical chemistry in Dr. Aurora E. Clark’s group at Washington State University. His doctoral research is primarily focused on the application of computational and theoretical chemistry to determine physical properties of disordered solid systems using density functional theory and cluster expansion methods.

An Introduction to Catastrophe Theory

Abstract: In this video, I give an introduction to some basic concepts from catastrophe theory. The goal of the video is to expose the viewer to the important ideas of catastrophe theory by using illustrative examples and visual simulations while avoiding most of the mathematical formalities and jargon. A portion of the video is devoted to introducing how one might use mathematics to model such phenomena with functions, and there are supplemental visualizations.

About the Author: Connor McCranie is a 4th year graduate student in mathematics at CU Boulder. His interests include topology, category theory, and number theory. He has been working as an assistant under Professor Markus Pflaum for 3 semesters studying catastrophe theory in relation to the DELTA project.