Physical Sciences and Mathematics Commons^™

Thermodynamics Of Ligand Binding And Global Structural Stability Of Human Serum Albumin, Matthew Walter Eskew

Dissertations and Theses

Protein structure is integral to its function. For the past 70 years differential scanning calorimetry has been used to measure protein structural stability. More recently it has been used to study macromolecular interactions. Interactions between proteins and ligands can manifest on differential scanning calorimetry melting curves or thermograms. Utilizing differential scanning calorimetry thermograms to detect or diagnose diseases has been a major goal in disease diagnostics. However, correlating specific ligand-protein interactions, as manifested in a thermogram, with a disease-specific plasma thermogram, has proven elusive.

Modified human serum albumin was utilized to develop a process to capture and retrieve ligands from …

Reconsidering The Foundations Of Thermodynamics From An Engineering Perspective, Terry Bristol

Mathematics and Statistics Faculty Publications and Presentations

Currently, there are two approaches to the foundations of thermodynamics. One, associated with the mechanistical Clausius-Boltzmann tradition, is favored by the physics community. The other, associated with the post-mechanical Carnot tradition, is favored by the engineering community. The bold hypothesis is that the conceptual foundation of engineering thermodynamics is the more comprehensive. Therefore, contrary to the dominant consensus, engineering thermodynamics (ET) represents the true foundation of thermodynamics. The foundational issue is crucial to a number of unresolved current and historical issues in thermodynamic theory and practice. ET formally explains the limited successes of the ‘rational mechanical’ approaches as idealizing special …

Geothermometry Of Two Cascade Geothermal Systems, Donnel Alexander Malkemus

Dissertations and Theses

For this thesis I applied classical and multi-component geothermometry techniques to new water chemistry data from Breitenbush Hot Springs, Oregon and the Wind River Valley, Washington. A total of 20 well, spring, and stream samples from Breitenbush Hot Springs and 4 spring samples from the Wind River Valley were collected and analyzed for major, minor, and select trace anions and cations, as well as stable oxygen and hydrogen isotopes. I used two computer programs, GeoT and RTEst, to conduct multi-component geothermometry reservoir condition estimation on each water sample. Water chemistry data from Breitenbush Hot Springs indicates a range of thermal, …

Discontinuities In Hygroscopic Growth Below And Above Water Saturation For Laboratory Surrogates Of Oligomers In Organic Atmospheric Aerosols, Natasha Hodas, Andreas Zuend, Katherine Schilling, Thomas Berkemeier, Manabu Shiraiwa, Richard C. Flagan, John H. Seinfeld

Environmental Science and Management Faculty Publications and Presentations

Discontinuities in apparent hygroscopicity below and above water saturation have been observed for organic and mixed organic–inorganic aerosol particles in both laboratory studies and in the ambient atmosphere. However, uncertainty remains regarding the factors that contribute to observations of low hygroscopic growth below water saturation but enhanced cloud condensation nuclei (CCN) activity for a given aerosol population. Utilizing laboratory surrogates for oligomers in atmospheric aerosols, we explore the extent to which such discontinuities are influenced by organic component molecular mass and viscosity, non-ideal thermodynamic interactions between aerosol components, and the combination of these factors. Measurements of hygroscopic growth under subsaturated …

Approximate Equations Of State In Two-Temperature Plasma Mixtures, John D. Ramshaw, Andrew W. Cook

Physics Faculty Publications and Presentations

Approximate thermodynamic state relations for multicomponent atomic and molecular gas mixtures are often constructed by artificially partitioning the mixture into its constituent materials and requiring the separated materials to be in temperature and pressure equilibrium. Iterative numerical algorithms have been employed to enforce this equilibration and compute the resulting approximate state relations in single-temperature mixtures. In partially ionized gas mixtures, there is both theoretical and empirical evidence that equilibrating the chemical potentials, number densities, or partial pressures of the free electrons is likely to produce more accurate results than equilibrating the total pressures. Moreover, in many situations of practical interest …

Supplementary Balance Laws For Cattaneo Heat Propagation, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work we determine for the Cattaneo heat propagation system all the supplementary balance laws (conservation laws ) of the same order (zero) as the system itself and extract the constitutive relations (expression for the internal energy) dictated by the Entropy Principle. The space of all supplementary balance laws (having the functional dimension 8) contains four original balance laws and their deformations depending on 4 functions of temperature (λ⁰(ϑ),K^A (ϑ), A = 1, 2, 3). The requirements of the II law of thermodynamics leads to the exclusion of three functional degrees (K^A= 0, A …

Model For Acid-Base Chemistry In Nanoparticle Growth (Mabnag), Taina Yli-Juuti, Kelley Barsanti, L. Hildebrandt Ruiz, Antti-Jussi Kieloaho, U. Makkonen, Tuukka Petäjä, Taina Ruuskanen, Markku Kulmala, Ilona Riipinen

Civil and Environmental Engineering Faculty Publications and Presentations

Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapours condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth) was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential …

Balance Systems And The Variational Bicomplex, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work we show that the systems of balance equations (balance systems) of continuum thermodynamics occupy a natural place in the variational bicomplex formalism. We apply the vertical homotopy decomposition to get a local splitting (in a convenient domain) of a general balance system as the sum of a Lagrangian part and a complemental "pure non-Lagrangian" balance system. In the case when derivatives of the dynamical fields do not enter the constitutive relations of the balance system, the "pure non-Lagrangian" systems coincide with the systems introduced by S. Godunov [Soviet Math. Dokl. 2 (1961), 947–948] and, later, asserted as …

Supplementary Balance Laws And The Entropy Principle, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work we study the mathematical aspects of the development in the continuum thermodynamics known as the “Entropy Principle”. It started with the pioneering works of B.Coleman, W.Noll and I. Muller in 60th of XX cent. and got its further development mostly in the works of G. Boillat, I-Shis Liu and T.Ruggeri. “Entropy Principle” combines in itself the structural requirement on the form of balance laws of the thermodynamical system (denote such system (C)) and on the entropy balance law with the convexity condition of the entropy density. First of these requirements has pure mathematical form defining so called …

Electrical Detection Of The Temperature Induced Melting Transition Of A Dna Hairpin Covalently Attached To Gold Interdigitated Microelectrodes, Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini Bhandiwad, David R. Evans, Raj Solanki, Albert S. Benight

Chemistry Faculty Publications and Presentations

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded …

The Indefinite Metric Of R. Mrugala And The Geometry Of The Thermodynamical Phase Space, Serge Preston, James Vargo

Mathematics and Statistics Faculty Publications and Presentations

We study an indefinite metric G which was introduced by R. Mrugala and is defined on the contact phase space (P, θ) of a homogeneous thermodynamical system. We describe the curvature properties and the isometry group of the metric G. We established an isomorphism of the space (P, θ, G) with the Heisenberg Lie group H_n, endowed with the right invariant contact structure and the right invariant indefinite metric. The lift of the metric G to the symplectization of contact space (P, θ) and its properties are studied. Finally we introduce the "hyperbolic projectivization" of the space …

Dna Multiplex Hybridization On Microarrays And Thermodynamic Stability In Solution: A Direct Comparison, Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, Albert S. Benight

Chemistry Faculty Publications and Presentations

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to …

Curvature Of The Weinhold Metric For Thermodynamical Systems With 2 Degrees Of Freedom, Manuel Santoro, Serge Preston

Mathematics and Statistics Faculty Publications and Presentations

In this work the curvature of Weinhold (thermodynamical) metric is studied in the case of systems with two thermodynamical degrees of freedom. Conditions for the Gauss curvature R to be zero, positive or negative are worked out. Signature change of the Weinhold metric and the corresponding singular behavior of the curvature at the phase boundaries are studied. Cases of systems with the constant C_v, including Ideal and Van der Waals gases, and that of Berthelot gas are discussed in detail.

Simple Approximation For Thermal Diffusion In Ionized Gas Mixtures, John D. Ramshaw

Physics Faculty Publications and Presentations

A simple approximation for thermal diffusion in gas mixtures was recently proposed [1]. This approximation was based upon relations valid for rigid spheres. It is therefore appropriate for molecules with steep repulsive potentials, but not for ionized species interacting via the Coulomb potential. Here we formulate an analogous approximation for ionized species and free electrons. The resulting thermal diffusion coefficients differ in sign from those for hard molecules.

Numerical Simulation Of Nonequilibrium Effects In An Argon Plasma Jet, C. H. Chang, John D. Ramshaw

Physics Faculty Publications and Presentations

Departures from thermal (translational), ionization, and excitation equilibrium in an axisymmetric argon plasma jet have been studied by two?dimensional numerical simulations. Electrons, ions, and excited and ground states of neutral atoms are represented as separate chemical species in the mixture. Transitions between excited states, as well as ionization/recombination reactions due to both collisional and radiative processes, are treated as separate chemical reactions. Resonance radiation transport is represented using Holstein escape factors to simulate both the optically thin and optically thick limits. The optically thin calculation showed significant underpopulation of excited species in the upstream part of the jet core, whereas …

Self-Consistent Effective Binary Diffusion In Multicomponent Gas Mixtures, John D. Ramshaw

Physics Faculty Publications and Presentations

The correct treatment of diffusion in multicomponent gas mixtures requires solution of a linear system of equations for the diffusive mass fluxes relative to the mass-averaged velocity of the mixture. Effective binary diffusion approximations are often used to avoid solving this system. These approximations are generally internally inconsistent in the sense that the approximate diffusion fluxes do not properly sum to zero. The origin of this inconsistency is identified, and a general procedure for removing it is presented. This procedure applies equally to concentration, forced, pressure, and thermal diffusion, either separately or in combination. It is used to obtain a …

Dielectric Saturation In Dipolar Fluids. I. The Single-Molecule Distribution Function, John D. Ramshaw

Physics Faculty Publications and Presentations

The functional-derivative formalism is used to investigate the form of the equilibrium single-molecule distribution function n(1) in a finite fluid system of rigid polar molecules subjected to a strong external electric field that varies slowly with position. The investigation is based on the assumption that the long-range asymptotic behavior of the direct correlation function is independent of the external field, and is hence the same as in the unperturbed fluid. This assumption implies that n(1) has the form of a single-molecule Boltzmann factor in which the interaction energy is that of a deformable quasidipole with the local Lorentz electric field …

Debye–Hückel Theory For Particles Of Arbitrary Electrical Structure, John D. Ramshaw

Physics Faculty Publications and Presentations

Classical linearized Debye–Hückel theory is formulated for a finite fluid system, of arbitrary shape, composed of rigid particles with arbitrary internal electrical structure. The multipole description is eschewed in favor of the more basic description of a particle in terms of its charge density function. This function is left arbitrary, so the particles may be charged or neutral, polar or nonpolar, etc. The theory implies that the direct correlation function c(12)=−v(12)/k T, where v(12) is the Coulomb interaction energy between the charge densities of particles 1 and 2. In the case of uncharged polar …

New Method For Generating Density Expansions, John D. Ramshaw

Physics Faculty Publications and Presentations

The calculus of finite differences is used to develop a new method for expressing the thermodynamic limit of a reasonably arbitrary statistical?mechanical average as a power series in the number density ?. The method is simple, straightforward, and purely analytic: it involves no intermediate expansion in powers of the activity and it avoids the use of graph theory. Moreover, the method is developed independently of the prescription for computing the statistical average, a fact which lends to the results an especially wide range of applicability. In particular, these results may be used in classical or quantum statistical mechanics, for intermolecular …