Precise knowledge of parton distribution functions (PDFs) is necessary to the accurate calculation of QCD observables initiated by hadrons. The deep inelastic scattering (DIS) and lepton pair production (LPP) processes are primary sources of information on PDFs. Recent global fits for PDFs have used DIS data from the large Bjorken $x$, moderate $Q^{2}$ region. It is known that there are large logarithms in this kinematic region that can be resummed using threshold resummation techniques. The purpose of this study is to investigate the effects of simultaneously including DIS and LPP threshold resummation in the determinations of PDFs. The analysis includes a study of the effects of the choice of resummation prescription and of current resummation methods used in the LPP rapidity and $x_{F}$ distributions. It is demonstrated theoretically and phenomenologically that the current resummation methods for such distributions are approximations that lose accuracy at high rapidities or $x_{F}$. The unapproximated resummation formalism is extended to the $\overline{\mathrm{MS}}$ scheme in the minimal and Borel prescriptions and used in conjunction with resummation in DIS to perform a global fit. The resultant PDF sets that correspond to two choices of resummation prescription are analyzed to determine the effect of threshold resummation on PDF fits and its theoretical uncertainties. / A Dissertation submitted to the Department of Physics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2015. / April 1, 2015. / PDF, Prescription, Resummation, Threshold / Includes bibliographical references. / Joseph F. Owens, III, Professor Directing Thesis; Ettore Aldrovandi, University Representative; Laura Reina, Committee Member; Susan Blessing, Committee Member; Winston Roberts, Committee Member.

An inverse kinematic proton scattering experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) using the GRETINA-S800 detector system in conjunction with the Ursinus College liquid hydrogen target. $\gamma$-ray yields from the experiment were determined using geant4 simulations, generating state population cross sections. These cross sections were used to extract the delta_3 deformation length for the low-lying octupole vibration excitations in Ca-48,49 using the coupled channels analysis code fresco. Particle-core coupling in Ca-49 was studied in comparison to Ca-48 through determination of the neutron and proton deformation lengths. The total inverse kinematic proton scattering deformation lengths were evaluated for the low-lying octupole vibration excitations in Ca-48,49 to be delta_3(Ca-48, 3^-_1) = 1.0(2)fm, delta_3(Ca-49, 9/2^+_1) = 1.2(1)fm, delta_3 (Ca-49, 9/2^+_1) = 1.5(2)fm, delta_3(Ca-49, 5/2^+_1) = 1.1(1)fm. Proton and neutron deformation lengths for two of these octupole states were also determined to be delta_p(Ca-48, 3^-_1) = 0.9(1)fm, delta_p (Ca-49, 9/2^+_1) = 1.0(1)fm, delta_n(Ca-48, 3^-_1) = 1.1(3)fm, and delta_n(Ca-49, 9/2^+_1) = 1.3(3)fm. Additionally, the ratios of the neutron to proton transition matrix elements were also determined for these two states to be M_n/M_p(Ca-48, 3^-_1) = 1.7(6) and M_n/M_p(Ca-49, 9/2^+_1) = 2.0(5). Statistically, the derived values for these two nuclei are nearly identical. / A Dissertation submitted to the Department of Physics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / July 8, 2015. / deformation, deformation length, nuclear, octupole, vibration, γ-ray spectroscopy / Includes bibliographical references. / Paul Cottle, Professor Directing Dissertation; Alec Kercheval, University Representative; Jianming Cao, Committee Member; Jorge Piekarewicz, Committee Member; Mark Riley, Committee Member.

Anthracis Repressor (AntR) is a Mn(II) activated DNA binding protein that is involved in the regulation of Mn(II) homeostasis in Bacillus anthracis. AntR is a member of the Diphtheria Toxin Repressor (DtxR) family of proteins. These proteins function as sensors of intracellular Fe(II) or Mn(II) levels and effect the metal regulated expression of many genes, frequently including virulence related genes. Our studies on AntR focus on metal regulated activation of the protein. We have determined the Mn(II) binding stoichiometry, equilibrium binding constants, and associated kinetic rate constants in AntR using a variety of electron paramagnetic resonance methods. Two divalent manganese ions were observed to bind AntR with positive cooperativity and apparent dissociation constants of 210 ± 18 μM and 16.6 ± 1.0 μM. Binding rates were in the sub-millisecond range, and dissociation rates were characterized by rate constants 35.7 ± 12.1 s-1 and 0.115 ± 0.009 s-1. We probed the nature of the metal binding site with EPR for comparison with the crystal structures of homologous manganese transport regulator (MntR) from Bacillus subtilis. The spectra were not consistent with a binuclear Mn(II) cluster as seen in MntR structures. Gel filtration, continuous wave EPR, and Pulsed EPR methods were used to investigate possible structural changes in response to metal binding. We found that AntR is exclusively dimeric in absence of Mn(II). Double electron-electron resonance (DEER) was employed to measure spin-spin distance of strategically placed nitroxide spin labels in dimeric AntR. To realize the full potential of DEER, an analysis software with graphical user interface was developed. The data indicated the presence of multiple conformations for each spin label pair in apo-AntR. Metal binding had little effect on these conformations, except near the putative DNA-binding helixes, where metal binding sharpened the distribution of conformers, and decreased the distance between DNA binding regions of AntR dimer. We also showed that the AntR backbone dynamics change considerably upon metal binding. A structure model for AntR was built from homology to MntR, and the experimentally measured distances were simulated. This model only partially agreed with the DEER results, suggesting structural differences between AntR and MntR. These results allow us to develop a model for the Mn(II) induced activation of the repressor. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Spring Semester, 2007. / January 12, 2007. / Manganese, MntR / Includes bibliographical references. / Piotr G. Fajer, Professor Co-Directing Dissertation; Timothy M. Logan, Professor Co-Directing Dissertation; Michael Blaber, Outside Committee Member; Richard Bertram, Committee Member; Hugh Nymeyer, Committee Member.

The Iron-dependent Regulator (IdeR) is a 230-amino acid transcriptional repressor that regulates iron homeostasis, oxidative stress response and virulence in Mycobacterium tuberculosis. The importance of IdeR for mycobacterial metabolism, virulence, and survival in the host cell suggests that the protein may have a potential as a therapeutic target. The natural ligand for IdeR is Fe(II), but Ni(II), Co(II), Cd(II), Mn(II), and Zn(II) also bind to and activate the protein in vitro. Protein activation by metal is complex process involving metal-induced folding of the N-terminal domain, changes in the interaction between the N- and C-terminal domains, and formation of homodimers. The objective of this work was to characterize the molecular details of IdeR activation in vitro. The dimerization energetics were determined as a function of metal binding using equilibrium analytical ultracentrifugation. The dissociation constant was strongly dependent on the metal ligation state of the protein. Addition of Ni(II) induced changes in fluorescence intensity and emission maximum of the tryptophan residues that strongly depended on protein concentration. Mutational analysis suggested that both tryptophan residues in IdeR are sensitive to folding, dimerization and metal binding. Metal binding affinity was measured quantitatively using equilibrium dialysis. The results showed strongly positive cooperative binding of three equivalents of metal per monomer. Metal binding was not cooperative in an IdeR variant that showed reduced affinity for dimer formation. The results of this study establish the positive cooperative nature of metal binding by IdeR and suggest that dimerization contributes significantly to the cooperative binding. Equilibrium binding studies together with fluorescence titration and isothermal titration calorimetry experiments performed in metal binding mutants revealed equal importance of the primary and ancillary metal binding sites for cooperativity of metal binding, in contrast to the differential role of each site in repressor activity in vitro. The strong coupling between metal binding and dimerization establishes "all or nothing" mechanism for regulation of repressor activity under the conditions of constantly changing free metal concentration, providing greater control over the metal-dependent DNA binding activity of IdeR. Our findings place specific constraints on the activation mechanism, simplifying the existing model. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Degree of Doctor of Philosophy. / Fall Semester, 2006. / July 13, 2006. / Dimerization, Ligand Binding, Cooperativity, Repressor / Includes bibliographical references. / Timothy M. Logan, Professor Directing Dissertation; Albert E. Stiegman, 1953-, Outside Committee Member; Michael Blaber, Committee Member; Piotr G. Fajer, Committee Member; Hong Li, Committee Member.

Cell adhesion assemblies occur at sites where cells either contact each other or components related to the extracellular matrix. They provide the structural integrity needed to support nonmigrating cells via a host of transmembraneous proteins. In addition to their structural role, these transmembrane receptors also establish a system of communicating with the cytoskeleton. One of the primary receptors found on the surface of stationary cells is the fibronectin receptor, also known as the a5b1-integrin. When bound to their extracellular ligand, fibronectin, these integrins assume an " active" conformation. This external binding event is coordinated with a series of physical changes that are translated through the transmembrane portion of the receptor and passed along to its cytoplasmic domain. Inside the cell, these perturbations cause a series of structural changes that allow the F-actin cytoskeleton to be linked to the integrin's cytoplasmic domain. Our interests lie in visualizing the macromolecular assemblies of the cytoskeletal components that support this linkage. The method we used to observe these adhesive complexes is transmission electron microscopy (TEM). We used the lipid monolayer crystallization technique for a dual purpose: 1) as a means of concentrating protein at the air:water interface, providing a crystallization surface; 2) to mimic the cytoplasmic leaflet, which contains a hydrophobic lipid layer on top of a bulk aqueous phase. Therefore, preparing an ordered EM specimen with these characteristics gives us a tool to study numerous biological systems. In this project specifically, we synthesized the integrin cytoplasmic domain with a histidine (His)-tag at its N-terminus and bound it to a lipid monolayer containing a nickel-chelating group. This causes the integrin to assume an orientation that represents its native conformation at the cell membrane. We were able to produce EM specimens that contained this integrin domain along with other cytoskeletal proteins, such as talin, a-actinin, vinculin and F-actin. In particular, the b1-integrin:a-actinin and the b1-integrin:aactinin: vinculin samples formed ordered arrays that we used to make frozen-hydrated specimens. We collected EM images of untilted samples and calculated their averaged 2-D projections. Additionally, we produced a 3-D reconstruction of the b1-integrin:a-actinin:vinculin assembly by collecting images of samples tilted up to 70o. Using molecular modeling software, in combination with information deposited into various protein databases, we created atomic models of both the b1-integrin as well as the vinculin-head piece. The docking of these models into our 3-D Cryo-EM map was quantified and refined to produce an atomic model for our assembly. Overall, this combination of imaging and model building establishes a methodology of producing complexes of adhesive proteins whose spatial relationships are virtually unknown. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2003. / March 27, 2003. / Intracellular and Extracellular Scaffolding, Adhesion / Includes bibliographical references. / Kenneth A. Taylor, Professor Directing Dissertation; Thomas M. Roberts, Outside Committee Member; Michael Blaber, Committee Member; Kenneth H. Roux, Committee Member; Thomas C. S. Keller, III, Committee Member.

Measurements have been made of the n-n angular correlation for neutrons emitted in spontaneous fission of ²⁵²Cf and thermal-neutron- induced fission of ²³⁵U. The dependence of the angular correlation on the neutron detection threshold energy was investigated. These measurements and other experimental data on the fission spectrum and the neutron angular distribution are compared with Monte Carlo calculations based on the evaporation model. It is apparent that a model assuming isotropic evaporation of all neutrons from the moving fragments cannot adequately explain the observed distributions. No evidence was found favouring the emission of a fraction of the neutrons isotropically at scission, or during the fragment acceleration period.

The n-d breakup cross section has been measured at eleven energies. between 8 and 22 MeV by integrating the energy distributions of breakup protons in a deuterated scintillator. The breakup protons were separated from the recoil deuterons by pulse shape discrimination. A comparison of these measurements with recent calculations favours those performed with local potentials.

Bibliography: p. 128-135. / The polarization in n-d scattering has been measured at incident energies 7.9, 16.4, and 21.6 MeV using neutrons from the ⁹Be(α,n) ¹²C and ³H(d,n) ⁴He reactions. The polarization analyzer was a deuterated anthracene scintillation crystal. Recoil deuterons from n-d elastic scattering within the crystal were studied and pulse shape discrimination (PSD) was used to determine the left-right asymmetry of the recoils. The experimental method depends on the fact that the PSD response of the crystal is sensitive to the direction of the recoil deuteron relative to the crystal axes. The results obtained are compared with theoretical calculations from the literature and with other measurements. A comparison of the n-d and p-d polarization data reveals no evidence of breaking of the charge symmetry of nuclear forces.

Bibliography p. 214-226. / Exclusive measurements have been made of the reactions ⁴He(p,2p ), (p,pd), (p,pt) and (p,ph) at 100 MeV. The primary protons were measured at two angles, 45° and 60°, in coincidence with secondary protons, deuterons, tritons or helions covering a wide range of angles on the opposite side of the beam, from -15° to -90° in plane, and from 0° to 30° out-of-plane. The purpose of the experiment was to explore the validity of the Distorted Wave Impulse Approximation (DWIA) as a description of these quasifree knockout reactions, at all geometries where the knockout cross section is significant. Six particle telescopes, each consisting of two silicon detectors and a NaI detector, were used to measure the coincident particles. The experimental data are presented in the form of energy-sharing distributions, which were generated by projecting the two-dimensional quasifree knockout loci onto the energy axis of the primary proton. The comparison between these energy-sharing distributions and the curves calculated by means of the DWIA is satisfactory for all geometries, except at the most forward secondary angles for the (p,pt) and (p,ph) reactions. It is concluded that the DWIA is an adequate formalism for modelling the quasifree knockout reactions induced by 100 MeV protons on ⁴He. Based on this conclusion, the total contribution of quasifree knockout to the existing inclusive (p,p') spectra has been calculated by integrating the DWIA cross sections over the solid angles of the secondary particles. The spectroscopic factors used were those extracted from the coincidence data. For the (p,pn) reaction, it was assumed that the spectroscopic factors were the same as for (p,2p). It is found that 70 ± 10% of the inclusive continuum yields is attributable to quasifree scattering, with ~30% arising from multiple scattering. At low energies of the scattered proton, the knockout of nucleons constitutes over 90% of the quasifree component, whereas at high energies the knockout of deuterons, tritons and helions dominates the yield. Thus the absence of discernable quasifree peaks in the inclusive spectra is probably due to the cluster knockout contributions filling in the yield at higher energies.

We study high-energy approximations to nuclear scattering. These are based on expansions of the free-particle propagator. We distinguish the eikonal expansion and the Fresnel expansion and interpret their physical meaning in optical terms. A "Fresnel approximation" is defined as a partial sum of the eikonal expansion which describes Fresnel diffraction effects. In Fresnel approximation we derive, by means of a unitary transformation, a closed representation of the scattering amplitude which is formally similar to the corresponding expression irt Glauber's high-energy scattering theory. The corrections to the Glauber model of first order in the reciprocal wave number are given by the second-order eikbnal approximation. These are evaluated explicitly for high energy elastic scattering of protons from light nuclei (⁴He, ¹²C, ¹⁶O).