Date of Graduation


Document Type


Degree Name

Master of Science in Computer Science (MS)

Degree Level



Computer Science & Computer Engineering


Matthew J. Patitz

Committee Member

David M. Ford

Second Committee Member

Khoa Luu

Third Committee Member

Lu Zhang


Diffusion Maps, Dimensionality Reduction, Neural Networks


This work employs tools and methods from computer science to study clusters comprising a small number N of interacting particles, which are of interest in science, engineering, and nanotechnology. Specifically, the thermodynamics of such clusters is studied using techniques from spectral graph theory (SGT) and machine learning (ML). SGT is used to define the structure of the clusters and ML is used on ensembles of cluster configurations to detect state variables that can be used to model the thermodynamic properties of the system. While the most fundamental description of a cluster is in 3N dimensions, i.e., the Cartesian coordinates of the particles, the ML results demonstrate that sub-spaces of much lower dimension can describe the observed structural motifs. Furthermore, these sub-spaces correlate with meaningful physical variables such as radius of gyration r g and discrete connectivity c, which can be used as state variables in thermodynamic property descriptions. The overarching theme of this thesis is to develop the practice of utilizing data-driven computational techniques to solve problems in natural sciences. Code for this project can be found at