Physical Sciences and Mathematics Commons^™

Predicting The Hydration Free Energy Of Small Alkanes And Alcohols From Custom, Electronic Structure-Based Force Fields, T. Ryan Rogers

Graduate Theses and Dissertations

Mathematical theories reveal the fundamental physics involved in experimentalphenomena. Computer models of such theories are routinely used to corroborate or explain experiments and predict properties of chemical systems. Therefore, an important effort in computational chemistry is the development of more accurate and efficient chemical models. Current-generation models are only beginning to approach experimental-quality predictions of hydration free energies (HFEs).Using computations of quantum mechanical (QM) forces and classical simulations based on these forces, I investigate models to predict several properties of solutes and solutions. This dissertation is a collection of projects exemplifying methods used to gain insight into chemical systems.

Simulations …

Protein Conformational Entropy Is Not Slaved To Water, Bryan S Marques, Matthew A Stetz, Christine Jorge, Kathleen G Valentine, A Joshua Wand, Nathaniel V Nucci

Faculty Scholarship for the College of Science & Mathematics

Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side …

Specificity Of Ssb Binding To Its Interacting Proteins And Multiple Allosteric Effects Of Ssb C-Terminal Tail On Assembly And Dna Binding Of E. Coli Recor Proteins, Min Kyung Shinn

Arts & Sciences Electronic Theses and Dissertations

The homo-tetrameric E. coli single strand (ss) DNA binding (SSB) protein is an essential component in DNA maintenance for its role in binding and protecting single stranded DNA intermediates via its N-terminal DNA binding domain (DBD). SSB also acts as a hub to recruit at least 17 SSB interacting proteins (SIPs) involved in DNA replication, recombination, and repair via its 9 amino acid C-terminal acidic tip region. A 56 amino acid intrinsically disordered linker connects the DBD and the acidic tip and plays a role in cooperative binding to ssDNA. Using isothermal titration calorimetry, I determined that the SSB-Ct peptides …

The Crisis Of Communication In The Information Age: Revisiting C.P. Snow's Two Cultures In The Era Of Fake News, Aaron Green

Irish Communication Review

The purpose of this paper is to revisit C.P. Snow’s “Two Cultures” lecture in light of the cultural dominance of information technology. The crisis of communication in the information age, whether in fake news, political polarisation or science denial, has come about because both scientific and literary cultures, in seeking a world without entropy, have inadvertently stumbled upon a world without meaning. In order to explain how this has happened, the paper first explores Snow's challenge: to describe the second law of thermodynamics. The paper then provides a description of entropy that is neutral with regard to thermodynamics and information, …

Contact In The Unitary Fermi Gas Across The Superfluid Phase Transition, S. Jensen, Christopher N. Gilbreth, Y. Alhassid

All Faculty Scholarship for the College of the Sciences

A quantity known as the contact is a fundamental thermodynamic property of quantum many-body systems with short-range interactions. Determination of the temperature dependence of the contact for the unitary Fermi gas of infinite scattering length has been a major challenge, with different calculations yielding qualitatively different results. Here we use finite-temperature auxiliary-field quantum Monte Carlo (AFMC) methods on the lattice within the canonical ensemble to calculate the temperature dependence of the contact for the homogeneous spin-balanced unitary Fermi gas. We extrapolate to the continuum limit for 40, 66, and 114 particles, eliminating systematic errors due to finite-range effects. We observe …

Testing A Thermodynamic Approach To Collective Animal Behavior In Laboratory Fish Schools, Julia A. Giannini, James G. Puckett

Physics and Astronomy Faculty Publications

Collective behaviors displayed by groups of social animals are observed frequently in nature. Understanding and predicting the behavior of complex biological systems is dependent on developing effective descriptions and models. While collective animal systems are characteristically nonequilibrium, we can employ concepts from equilibrium statistical mechanics to motivate the measurement of material-like properties in laboratory animal aggregates. Here, we present results from a new set of experiments that utilize high speed footage of two-dimensional schooling events, particle tracking, and projected static and dynamic light fields to observe and control the behavior of negatively phototaxic fish schools (Hemigrammus bleheri). First, …