2020-
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Browsing 2020- by Author "Achter, Jeff, committee member"
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Item Open Access Molecular configurations and persistence: branched alkanes and additive energies(Colorado State University. Libraries, 2022) Story, Brittany M., author; Adams, Henry, advisor; Shipman, Patrick, committee member; Achter, Jeff, committee member; Fremstad, Anders, committee memberEnergy landscapes are high-dimensional functions that encapsulate how certain molecular properties affect the energy of a molecule. Chemists use disconnectivity graphs to find transition paths, the lowest amount of energy needed to transfer from one energy minimum to another. But disconnectivity graphs fail to show not only some lower-dimensional features, such as transition paths with an energy value only slightly higher than the minimum transition path, but also all higher-dimensional features. Sublevelset persistent homology is a tool that can be used to capture other relevant features, including all transition paths. In this paper, we will use sublevelset persistent homology to find the structure of the energy landscapes of branched alkanes: tree-like molecules consisting of only carbons and hydrogens. We derive complete characterizations of the sublevelset persistent homology of the OPLS-UA energy function on two different families of branched alkanes. More generally, we explain how the sublevelset persistent homology of any additive energy landscape can be computed from the individual terms comprising that landscape.Item Open Access The conjugacy extension problem(Colorado State University. Libraries, 2021) Afandi, Rebecca, author; Hulpke, Alexander, advisor; Achter, Jeff, committee member; Pries, Rachel, committee member; Rajopadhye, Sanjay, committee memberIn this dissertation, we consider R-conjugacy of integral matrices for various commutative rings R. An existence theorem of Guralnick states that integral matrices which are Zp-conjugate for every prime p are conjugate over some algebraic extension of Z. We refer to the problem of determining this algebraic extension as the conjugacy extension problem. We will describe our contributions to solving this problem. We discuss how a correspondence between Z-conjugacy classes of matrices and certain fractional ideal classes can be extended to the context of R-conjugacy for R an integral domain. In the case of integral matrices with a fixed irreducible characteristic polynomial, this theory allows us to implement an algorithm which tests for conjugacy of these matrices over the ring of integers of a specified number field. We also describe how class fields can be used to solve the conjugacy extension problem in some examples.