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Final Master’s Thesis
April 11 @ 3:30 pm - 4:30 pm
Lelee Ounkham (A. Clark group) will present her final Master’s thesis at 3:30 pm in Fulmer 301B.
Zoom Link– https://wsu.zoom.us/j/179710472
GRAPH THEORETICAL AND PERSISTENT HOMOLOGY METHODS FOR UNDERSTANDING REACTIVITY IN RING POLYMER MOLECULAR DYNAMICS
Methods that incorporate nuclear quantum effects (NQEs) into statistical mechanical simulation have become increasingly accessible to the computational chemistry community within the last decade. As a specific case, ring polymer molecular dynamics (RPMD) is an approximate imaginary-time path integral based-quantum dynamical technique that maps the dynamics of quantum mechanical particles onto a system of classical beads harmonically interacting between neighboring beads. Although significant information is contained within the distribution and shape of the ring polymer description of an atom, much of the spatiotemporal analysis of RPMD trajectories relies upon correlation functions derived from the centroid of the ring polymer. Using graph theoretical and persistent homology methods, this thesis explores and develops new analysis methods to determine the influences of NQEs and understand their role in chemical reactivity. Since the description of the atom is based on the beads in the ring polymer, different atomic connectivity patterns are considered and can be analyzed in a probabilistic manner. Subsequently, weighted covalent bond networks are created and used to examine speciation and reactivity within acidic solutions. Additionally, persistent homology methods have been developed to study the shapes and shape fluctuations of the ring polymers.