The studies presented here use the B- to Z-DNA transition and Z-DNA crystallization as model systems to determine the contribution of solvent interactions to macromolecular structures. The substituent groups of naturally occurring and modified nucleotide bases affect the hydration and thus the stability of right-handed B-DNA and left-handed Z-DNA. The free energy for alternating pyrimidine-purine sequences in the B- and Z-conformations are quantitated as solvent free energies (SFE) from their solvent-accessible surfaces. The effect of methylation of the C5 carbon of pyrimidine bases on the stability of Z-DNA was analyzed in comparisons of d(TA) versus d(UA) dinucleotides. In the minor groove, the N2 amino group of purine bases was examined by comparing the stability of d(CG) versus d(CI), and d(TA) versus d(TA') dinucleotides as Z-DNA. These comparisons correctly accounted for the observed effects of the major and minor groove substituent groups on the relative stability of Z-DNA. These predictions were confirmed by comparing the amount of salt required to crystallize various hexanucleotides as Z-DNA. The relative contribution of solvent and steric interactions in DNA assembly were studied crystallographically using an asymmetric hexanucleotide which assumes two discrete and discernible orientations in the crystal lattice. How this sequence orients in the lattice is a direct measure of the DNA-DNA interactions at the surface of the crystal. These interaction free energies were directly correlated with differences in solvation for 5 sequences where there was effectively no differences in steric interactions for the two orientations. In the singular case where a large steric clash was expected, the orientation was in fact determined by this interaction. The comparisons indicate that both solvent and van der Waals interactions are significant in DNA assembly with van der Waa ls interactions dominating in situations with large steric interactions. The analyses of the B- to Z-DNA transition and Z-DNA crystallization based on SFEs support the significance of solvent interactions in determining the structure and assembly of macromolecules. / Graduation date: 1995

Thesis (Ph. D.)--University of Chicago, 1922. / "Private edition, distributed by the University of Chicago libraries." Also available on the Internet. Also issued online.

Thesis (Ph. D.)--University of Chicago, 1912. / Vita. Also available on the Internet.

The adsorption equilibrium and kinetic behavior exhibited by β-lactoglobulin at silanized silicon surfaces of varying hydrophobicity were examined using ellipsometry. Adsorption equilibrium results were used to construct adsorption isotherms; the adsorbed mass of β-lactoglobulin was observed to increase with increasing surface hydrophobicity, within a defined range of hydrophobicity. Adsorption kinetics recorded for β-lactoglobulin on each surface were compared to the kinetic behavior predicted by a simple model for protein adsorption. The model described the data well in all cases, enabling interpretation of the kinetic behavior in terms of contact surface hydrophobicity influences on rate constants affecting protein attachment and unfolding at the interface. In particular, both experimental and simulation results seem to be in support of a hypothesis that rate constants defining protein arrival and conversion to an irreversibly adsorbed state increase with increasing surface hydrophobicity, while the rate constant defining desorption of protein from a reversibly adsorbed state decreases with increasing surface hydrophobicity. Contact surface hydrophobicity was quantified using contact angle analysis to determine the polar component of the work required to remove water from unit area of surface. Quantitative consideration of possible mass transfer influences on the observed adsorption rates supports the notion that the experiments were not conducted in a transport-limited regime; i.e., true kinetics were measured. / Graduation date: 1992

Variational method is used to investigate, at zero temperature, the deformed- Fermi-surfaces mechanism for solving the problem of superconducting pairing of two species of fermions (i.e., spin-up and -down) of mismatched Fermi surfaces due to the existence of a uniform exchange or Zeeman field. After analyzing the depairing regions in the whole three-dimensional parameter space, we obtain a trial groundstate wave-function as a function of the three variational parameters, one of which is the gap function. Then within the frame work of the weak-coupling BCS theory, the expectation value of the Hamiltonian of a conductor under an exchange or Zeeman field is derived, from which a gap equation is derived by differentiation. The influence of deformed Fermi surfaces on the chemical potential is then calculated. Computer programing is finally used to solve the gap equation, and find the minimum-energy state with respect to the remaining two variational parameters (δµ and z). These two parameters are better than the original parameters used in the trial Hamiltonian when compared with the FF state. And we also found if we keep the total number of electrons fixed, the system prefers an unchanged chemical potential and the ground state energy of the deformed-Fermi-surfaces state, which is found to be an angle dependent case of Sarma’s solution III, is no better than that of the unpolarized BCS state.

Variational method is used to investigate, at zero temperature, the deformed- Fermi-surfaces mechanism for solving the problem of superconducting pairing of two species of fermions (i.e., spin-up and -down) of mismatched Fermi surfaces due to the existence of a uniform exchange or Zeeman field. After analyzing the depairing regions in the whole three-dimensional parameter space, we obtain a trial groundstate wave-function as a function of the three variational parameters, one of which is the gap function. Then within the frame work of the weak-coupling BCS theory, the expectation value of the Hamiltonian of a conductor under an exchange or Zeeman field is derived, from which a gap equation is derived by differentiation. The influence of deformed Fermi surfaces on the chemical potential is then calculated. Computer programing is finally used to solve the gap equation, and find the minimum-energy state with respect to the remaining two variational parameters (δμ and z). These two parameters are better than the original parameters used in the trial Hamiltonian when compared with the FF state. And we also found if we keep the total number of electrons fixed, the system prefers an unchanged chemical potential and the ground state energy of the deformed-Fermi-surfaces state, which is found to be an angle dependent case of Sarma's solution III, is no better than that of the unpolarized BCS state.

Diss.--Mathematik--Berlin--Technische Universität, 1998. / Notes bibliogr.

Dissertation--Åbo Akademi university, 2003. / Notes bibliogr.

Thesis (Ph. D.)--University of Alberta, 2009. / Title from pdf file main screen (viewed on Dec. 22, 2009). "A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Applied Mathematics, Department of Mathematical and Statistical Sciences, University of Alberta." Includes bibliographical references.

Thèse de doctorat : Sciences Odontologiques : Strasbourg : 2009. / Thèse soutenue sur un ensemble de travaux. Titre provenant de l'écran-titre. Bibliogr. 9 p.