Diversification of the tropical Pacific avifauna

I investigated the origins and diversification of Pacific avifaunas. Chapters 1, 2, and 4 elucidate the evolutionary history of three classically polytypic species complexes of Pacific island birds using multilocus phylogeographic approaches. The focal taxa were: Ceyx lepidus (Aves: Alcedinidae), Pachycephala pectoralis (Aves: Pachycephalidae), and Todiramphus chloris (Aves: Alcedinidae). In chapter 3, I examined the systematic relationships of 14 species of Pacific honeyeaters (Aves: Meliphagidae) relative to continental lineages. Each of these studies revealed novel biogeographical patterns heretofore underappreciated in Pacific birds. All three species complexes underwent rapid diversification with extensive genetic and phenotypic differentiation across widespread island archipelagos spanning thousands of kilometers from southeast Asia to Polynesia. This pattern was evidenced by phylogenies with short basal internodes, long stem lineages, and shallow divergences within each taxon. Todiramphus was noteworthy because it has attained extensive reproductive isolation, despite the recency of the radiation, as evidenced by multiple sympatric taxa throughout the Pacific. The work on meliphagid honeyeaters found extensive paraphyly of Pacific lineages with respect to their presumed continental congeners. I found evidence for a Central Polynesian radiation that included taxa from the eastern Solomon Islands, Fiji, Samoa, and Tonga. Throughout this dissertation I draw inferences on the processes of origination, diversification, and extinction in Pacific avifaunas using a comparative framework across multiple lineages at different scales of differentiation

Gluon Thermodynamics at Intermediate Coupling

We calculate the thermodynamic functions of Yang-Mills theory to three-loop order using the hard-thermal-loop perturbation theory reorganization of finite temperature quantum field theory. We show that at three-loop order hard-thermal-loop perturbation theory is compatible with lattice results for the pressure, energy density, and entropy down to temperatures T ~ 2 - 3 T_c.Comment: 4 pages, 3 figures; v2 - published version

Mixing of ultracold atomic clouds by merging of two magnetic traps

We demonstrate a method to make mixtures of ultracold atoms that does not make use of a two-species magneto-optical trap. We prepare two clouds of 87Rb atoms in distinct magnetic quadrupole traps and mix the two clouds by merging the traps. For correctly chosen parameters the mixing can be done essentially without loss of atoms and with only minor heating. The basic features of the process can be accounted for by a classical simulation of particle trajectories. Such calculations indicate that mixing of different mass species is also feasible, opening the way for using the method as a starting point for making quantum gas mixtures.Comment: 12 pages, 13 figures. Fig. 10 corrected. Fig. 13 updated with more points and better statistics. A couple of paragraphs rephrased and typos corrected. References update

Screened Perturbation Theory to Three Loops

The thermal physics of a massless scalar field with a phi^4 interaction is studied within screened perturbation theory (SPT). In this method the perturbative expansion is reorganized by adding and subtracting a mass term in the lagrangian. We consider several different mass prescriptions that generalize the one-loop gap equation to two-loop order. We calculate the pressure and entropy to three-loop order and the screening mass to two-loop order. In contrast to the weak-coupling expansion, the SPT-improved approximations appear to converge even for rather large values of the coupling constant.Comment: 30 pages, 10 figure

Mass Expansions of Screened Perturbation Theory

The thermodynamics of massless phi^4-theory is studied within screened perturbation theory (SPT). In this method the perturbative expansion is reorganized by adding and subtracting a mass term in the Lagrangian. We analytically calculate the pressure and entropy to three-loop order and the screening mass to two-loop order, expanding in powers of m/T. The truncated m/T-expansion results are compared with numerical SPT results for the pressure, entropy and screening mass which are accurate to all orders in m/T. It is shown that the m/T-expansion converges quickly and provides an accurate description of the thermodynamic functions for large values of the coupling constant.Comment: 22 pages, 10 figure

On the Inelastic Collapse of a Ball Bouncing on a Randomly Vibrating Platform

We study analytically the dynamics of a ball bouncing inelastically on a randomly vibrating platform, as a simple toy model of inelastic collapse. Of principal interest are the distributions of the number of flights n_f till the collapse and the total time \tau_c elapsed before the collapse. In the strictly elastic case, both distributions have power law tails characterised by exponents which are universal, i.e., independent of the details of the platform noise distribution. In the inelastic case, both distributions have exponential tails: P(n_f) ~ exp[-\theta_1 n_f] and P(\tau_c) ~ exp[-\theta_2 \tau_c]. The decay exponents \theta_1 and \theta_2 depend continuously on the coefficient of restitution and are nonuniversal; however as one approches the elastic limit, they vanish in a universal manner that we compute exactly. An explicit expression for \theta_1 is provided for a particular case of the platform noise distribution.Comment: 32 page

The Equation of State for Dense QCD and Quark Stars

We calculate the equation of state for degenerate quark matter to leading order in hard-dense-loop (HDL) perturbation theory. We solve the Tolman-Oppenheimer-Volkov equations to obtain the mass-radius relation for dense quark stars. Both the perturbative QCD and the HDL equations of state have a large variation with respect to the renormalization scale for quark chemical potential below 1 GeV which leads to large theoretical uncertainties in the quark star mass-radius relation.Comment: 7 pages, 3 figure

Hydrographic Surveys for Six Water Bodies in Eastern Nebraska, 2005–07

The U.S. Geological Survey, in cooperation with the Nebraska Department of Environmental Quality, completed hydrographic surveys for six water bodies in eastern Nebraska: Maskenthine Wetland, Olive Creek Lake, Standing Bear Lake, Wagon Train Lake and Wetland, Wildwood Lake, and Yankee Hill Lake and sediment basin. The bathymetric data were collected using a boat-mounted survey-grade fathometer that operated at 200 kHz, and a differentially corrected Global Positioning System with antenna mounted directly above the echo-sounder transducer. Shallow-water and terrestrial areas were surveyed using a Real-Time Kinematic Global Position¬ing System. The bathymetric, shallow-water, and terrestrial data were processed in a geographic information system to generate a triangulated irregular network representation of the bottom of the water body. Bathymetric contours were interpolated from the triangulated irregular network data using a 2-foot contour interval. Bathymetric contours at the conser¬vation pool elevation for Maskenthine Wetland, Yankee Hill Lake, and Yankee Hill sediment pond also were interpolated in addition to the 2-foot contours. The surface area and storage capacity of each lake or wetland were calculated for 1-foot intervals of water surface elevation and are tabulated in the Appendix for all water bodies

Three-loop HTL Free Energy for QED

We calculate the free energy of a hot gas of electrons and photons to three loops using the hard-thermal-loop perturbation theory reorganization of finite-temperature perturbation theory. We calculate the free energy through three loops by expanding in a power series in m_D/T, m_f/T, and e^2, where m_D and m_f are thermal masses and e is the coupling constant. We demonstrate that the hard-thermal-loop perturbation reorganization improves the convergence of the successive approximations to the QED free energy at large coupling, e ~ 2. The reorganization is gauge invariant by construction, and due to cancellation among various contributions, we obtain a completely analytic result for the resummed thermodynamic potential at three loops. Finally, we compare our result with similar calculations that use the Phi-derivable approach.Comment: 23 pages, 10 figures; v3 - typos corrected, additional discussions of systematics added; corresponds with published versio

Model-based analysis of N-glycosylation in Chinese hamster ovary cells

The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. The similarity of its glycosylation patterns to the human versions enable the products of this cell line favorable pharmacokinetic properties and lower likelihood of causing immunogenic responses. Because glycan structures are the product of the concerted action of intracellular enzymes, it is difficult to predict a priori how the effects of genetic manipulations alter glycan structures of cells and therapeutic properties. For that reason, quantitative models able to predict glycosylation have emerged as promising tools to deal with the complexity of glycosylation processing. For example, an earlier version of the same model used in this study was used by others to successfully predict changes in enzyme activities that could produce a desired change in glycan structure. In this study we utilize an updated version of this model to provide a comprehensive analysis of N-glycosylation in ten Chinese hamster ovary (CHO) cell lines that include a wild type parent and nine mutants of CHO, through interpretation of previously published mass spectrometry data. The updated N-glycosylation mathematical model contains up to 50,605 glycan structures. Adjusting the enzyme activities in this model to match N-glycan mass spectra produces detailed predictions of the glycosylation process, enzyme activity profiles and complete glycosylation profiles of each of the cell lines. These profiles are consistent with biochemical and genetic data reported previously. The model-based results also predict glycosylation features of the cell lines not previously published, indicating more complex changes in glycosylation enzyme activities than just those resulting directly from gene mutations. The model predicts that the CHO cell lines possess regulatory mechanisms that allow them to adjust glycosylation enzyme activities to mitigate side effects of the primary loss or gain of glycosylation function known to exist in these mutant cell lines. Quantitative models of CHO cell glycosylation have the potential for predicting how glycoengineering manipulations might affect glycoform distributions to improve the therapeutic performance of glycoprotein products