Interweaving Computational Chemistry and Visualization: Explorations into Molecular Processes, Simulation Analysis, and Visualization Design
Abstract
This thesis is a three-part exploration of both chemistry and computer science through the interweaving of computational chemistry and visualization in a research context. Motivating overarching themes in this thesis include the use of chemical simulations to advance chemical understanding, and visualization as a tool to help bridge the gap between possessing chemical simulation data and advancing chemical understanding. In Part I of this thesis, a set of novel visualizations are introduced to address data analysis challenges in the context of Molecular Dynamics simulations. Through these visualizations, aqueous hydroxyl radical chemistry is advanced (e.g., through characterization of a hydroxyl radical reaction), and concepts relevant to future chemical visualizations are revealed. In Part II, extensive simulations, detailed data analysis, and visualization are then combined to probe gas hydrate formation (a crystallization process amenable to simulation, and yet not fully understood). This work demonstrates that gas hydrate formation involves funnel-shaped potential energy landscapes, that the evolution of nascent hydrate phases can be structurally biased, and that microscopic details (e.g., guest-host interactions) can apparently impact behavior and composition of nascent mixed hydrate phases. The concepts of funnel-shaped potential energy landscapes and biased evolution are relevant to scientific understanding of crystallization more broadly beyond formation of gas hydrates. In order to support others as they design visualizations, Part III explores the role of emphasis in visualization, and introduces an alternative design approach for problem-driven visualization work. In addition to advancing chemical understanding and visualization, this thesis provides evidence that novel visualizations can help bridge the gap between possessing chemical data and achieving chemical understanding. This thesis is thus a multifaceted interdisciplinary exploration and discussion of chemical processes, visualizations and their role in chemical research, and visualization design.
Description
Keywords
Chemistry--Physical, Computer Science
Citation
Hall, K. (2017). Interweaving Computational Chemistry and Visualization: Explorations into Molecular Processes, Simulation Analysis, and Visualization Design (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/26619