A Visual Analytics Workflow for Detecting Transition Regions in Large Scale Molecular Dynamics Simulations
Description
Molecular Dynamics (MD) simulations are ubiquitous throughout the physical sci-ences; they are critical in understanding how particle structures evolve over time
given a particular energy function. A software package called ParSplice introduced a
new method to generate these simulations in parallel that has significantly inflated
their length. Typically, simulations are short discrete Markov chains, only captur-
ing a few microseconds of a particle’s behavior and containing tens of thousands of
transitions between states; in contrast, a typical ParSplice simulation can be as long
as a few milliseconds, containing tens of millions of transitions. Naturally, sifting
through data of this size is impossible by hand, and there are a number of visualiza-
tion systems that provide comprehensive and intuitive analyses of particle structures
throughout MD simulations. However, no visual analytics systems have been built
that can manage the simulations that ParSplice produces. To analyze these large
data-sets, I built a visual analytics system that provides multiple coordinated views
that simultaneously describe the data temporally, within its structural context, and
based on its properties. The system provides fluid and powerful user interactions
regardless of the size of the data, allowing the user to drill down into the data-set to
get detailed insights, as well as run and save various calculations, most notably the
Nudged Elastic Band method. The system also allows the comparison of multiple
trajectories, revealing more information about the general behavior of particles at different temperatures, energy states etc.
Date Created
The date the item was original created (prior to any relationship with the ASU Digital Repositories.)
2022
Agent
- Author (aut): Hnatyshyn, Rostyslav
- Thesis advisor (ths): Maciejewski, Ross
- Committee member: Bryan, Chris
- Committee member: Ahrens, James
- Publisher (pbl): Arizona State University