Doctor of Philosophy

dissertationHigh-performance supercomputers on the Top500 list are commonly designed around commodity CPUs. Most of the codes executed on these machines are message-passing codes using the message-passing toolkit (MPI). Thus it makes sense to look at these machines from a holistic systems architecture perspective and consider optimizations to commodity processors that make them more efficient in message-passing architectures. Described herein is a new User-Level Notification (ULN) architecture that significantly improves message-passing performance. The architecture integrates a simultaneous multithreaded (SMT) processor with a user-level network interface (NI) that can directly control the execution scheduling of threads on the processor. By allowing the network interface to control the execution of message handling code at the user level, the operating system (OS) related overhead for handling interrupts and user code dispatch related to notifications is eliminated. By using an SMT processor, message handling can be performed in one thread concurrent to user computation in other threads, thus most of the overhead of executing message handlers can be hidden. This dissertation presents measurements showing the OS overheads related to message-passing are significant in modern architectures and describes a new architecture that significantly reduces these overheads. On a communication-intensive real-world application, the ULN architecture provides a 50.9% performance improvement over a more traditional OS-based NIC and a 5.29-31.9% improvement over a best-of-class user-level NIC due to the user-level notifications

Durrington Walls to West Amesbury by way of Stonehenge: a major transformation of the Holocene landscape

A new sequence of Holocene landscape change has been discovered through an investigation of sediment sequences, palaeosols, pollen and molluscan data discovered during the Stonehenge Riverside Project. The early post-glacial vegetational succession in the Avon valley at Durrington Walls was apparently slow and partial, with intermittent woodland modification and the opening-up of this landscape in the later Mesolithic and earlier Neolithic, though a strong element of pine lingered into the third millennium BC. There appears to have been a major hiatus around 2900 cal BC, coincident with the beginnings of demonstrable human activities at Durrington Walls, but slightly after activity started at Stonehenge. This was reflected in episodic increases in channel sedimentation and tree and shrub clearance, leading to a more open downland, with greater indications of anthropogenic activity, and an increasingly wet floodplain with sedges and alder along the river’s edge. Nonetheless, a localized woodland cover remained in the vicinity of DurringtonWalls throughout the third and second millennia BC, perhaps on the higher parts of the downs, while stable grassland, with rendzina soils, predominated on the downland slopes, and alder–hazel carr woodland and sedges continued to fringe the wet floodplain. This evidence is strongly indicative of a stable and managed landscape in Neolithic and Bronze Age times. It is not until c 800–500 cal BC that this landscape was completely cleared, except for the marshy-sedge fringe of the floodplain, and that colluvial sedimentation began in earnest associated with increased arable agriculture, a situation that continued through Roman and historic times

Is the squeezing of relic gravitational waves produced by inflation detectable?

Grishchuk has shown that the stochastic background of gravitational waves produced by an inflationary phase in the early Universe has an unusual property: it is not a stationary Gaussian random process. Due to squeezing, the phases of the different waves are correlated in a deterministic way, arising from the process of parametric amplification that created them. The resulting random process is Gaussian but non-stationary. This provides a unique signature that could in principle distinguish a background created by inflation from stationary stochastic backgrounds created by other types of processes. We address the question: could this signature be observed with a gravitational wave detector? Sadly, the answer appears to be "no": an experiment which could distinguish the non-stationary behavior would have to last approximately the age of the Universe at the time of measurement. This rules out direct detection by ground and space based gravitational wave detectors, but not indirect detections via the electromagnetic Cosmic Microwave Background Radiation (CMBR).Comment: 17 pages, 4 Postscript figures, uses revtex, psfig, to be submitted to PRD, minor revisions - appendix B clarified, corrected typos, added reference

Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle

This work was funded by UK NERC grants to M.G.R. and A.J.M. an NERC studentship to D.J.P. the University of Georgia and a US NSF grant to A.J.M. and M.G.R.Parenting in the burying beetle Nicrophorus vespilloides is complex and, unusually, the sex and number of parents that can be present is flexible. Such flexibility is expected to involve specialized behaviour by the two sexes under biparental conditions. Here, we show that offspring fare equally well regardless of the sex or number of parents present. Comparing transcriptomes, we find a largely overlapping set of differentially expressed genes in both uniparental and biparental females and in uniparental males including vitellogenin, associated with reproduction, and takeout, influencing sex-specific mating and feeding behaviour. Gene expression in biparental males is similar to that in non-caring states. Thus, being ‘biparental’ in N. vespilloides describes the family social organization rather than the number of directly parenting individuals. There was no specialization; instead, in biparental families, direct male parental care appears to be limited with female behaviour unchanged. This should lead to strong sexual conflict.Publisher PDFPeer reviewe

Green's function for gravitational waves in FRW spacetimes

A method for calculating the retarded Green's function for the gravitational wave equation in Friedmann-Roberson-Walker spacetimes, within the formalism of linearized Einstein gravity is developed. Hadamard's general solution to Cauchy's problem for second-order, linear partial differential equations is applied to the FRW gravitational wave equation. The retarded Green's function may be calculated for any FRW spacetime, with curved or flat spatial sections, for which the functional form of the Ricci scalar curvature $R$ is known. The retarded Green's function for gravitational waves propagating through a cosmological fluid composed of both radiation and dust is calculated analytically for the first time. It is also shown that for all FRW spacetimes in which the Ricci scalar curvatures does not vanish, $R \neq 0$, the Green's function violates Huygens' principle; the Green's function has support inside the light-cone due to the scatter of gravitational waves off the background curvature.Comment: 9 pages, FERMILAB-Pub-93/189-

Properties of the Distant Kuiper Belt: Results from the Palomar Distant Solar System Survey

We present the results of a wide-field survey using the 1.2-m Samuel Oschin Telescope at Palomar Observatory. This survey was designed to find the most distant members of the Kuiper belt and beyond. We searched ~12,000 deg2 down to a mean limiting magnitude of 21.3 in R. A total number of 52 KBOs and Centaurs have been detected, 25 of which were discovered in this survey. Except for the re-detection of Sedna, no additional Sedna-like bodies with perihelia greater than 45 AU were detected despite sensitivity out to distances of 1000 AU. We discuss the implications for a distant Sedna- like population beyond the Kuiper belt, focusing on the constraints we can place on the embedded stellar cluster environment the early Sun may be have been born in, where the location and distribution of Sedna-like orbits sculpted by multiple stellar encounters is indicative of the birth cluster size. We also report our observed latitude distribution and implications for the size of the plutino population.Comment: 40 pages, 12 figures, 3 tables Accepted by Ap

Herpes Simplex Virus-1 Infection in Human Primary Corneal Epithelial Cells is Blocked by a Stapled Peptide that Targets Processive DNA Synthesis

Purpose: Acyclovir is most commonly used for treating ocular Herpes Keratitis, a leading cause of infectious blindness. However, emerging resistance to Acyclovir resulting from mutations in the thymidine kinase gene of Herpes Simplex Virus −1 (HSV-1), has prompted the need for new therapeutics directed against a different viral protein. One novel target is the HSV-1 Processivity Factor which is essential for tethering HSV-1 Polymerase to the viral genome to enable long-chain DNA synthesis. Methods: A series of peptides, based on the crystal structure of the C-terminus of HSV-1 Polymerase, were constructed with hydrocarbon staples to retain their alpha-helical conformation. The stapled peptides were tested for blocking both HSV-1 DNA synthesis and infection. The most effective peptide was further optimized by replacing its negative N-terminus with two hydrophobic valine residues. This di-valine stapled peptide was tested for inhibiting HSV-1 infection of human primary corneal epithelial cells. Results: The stapled peptides blocked HSV-1 DNA synthesis and HSV-1 infection. The unstapled control peptide had no inhibitory effects. Specificity of the stapled peptides was confirmed by their inabilities to block infection by an unrelated virus. Significantly, the optimized di-valine stapled peptide effectively blocked HSV-1 infection in human primary corneal epithelial cells with selectivity index of 11.6. Conclusions: Hydrocarbon stapled peptides that simulate the α-helix from the C-terminus of HSV-1 DNA polymerase can specifically block DNA synthesis and infection of HSV-1 in human primary corneal epithelial cells. These stapled peptides provide a foundation for developing a topical therapeutic for treating human ocular Herpes Keratitis. © 202

Evolution in the Disks and Bulges of Group Galaxies since z=0.4

We present quantitative morphology measurements of a sample of optically selected group galaxies at 0.3 < z < 0.55 using the Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) and the GIM2D surface brightness--fitting software package. The group sample is derived from the Canadian Network for Observational Cosmology Field Redshift survey (CNOC2) and follow-up Magellan spectroscopy. We compare these measurements to a similarly selected group sample from the Millennium Galaxy Catalogue (MGC) at 0.05 < z < 0.12. We find that, at both epochs, the group and field fractional bulge luminosity (B/T) distributions differ significantly, with the dominant difference being a deficit of disk--dominated (B/T < 0.2) galaxies in the group samples. At fixed luminosity, z=0.4 groups have ~ 5.5 +/- 2 % fewer disk--dominated galaxies than the field, while by z=0.1 this difference has increased to ~ 19 +/- 6 %. Despite the morphological evolution we see no evidence that the group environment is actively perturbing or otherwise affecting the entire existing disk population. At both redshifts, the disks of group galaxies have similar scaling relations and show similar median asymmetries as the disks of field galaxies. We do find evidence that the fraction of highly asymmetric, bulge--dominated galaxies is 6 +/- 3 % higher in groups than in the field, suggesting there may be enhanced merging in group environments. We replicate our group samples at z=0.4 and z=0 using the semi-analytic galaxy catalogues of Bower et al (2006). This model accurately reproduces the B/T distributions of the group and field at z=0.1. However, the model does not reproduce our finding that the deficit of disks in groups has increased significantly since z=0.4.Comment: Accepted for publication in MNRAS. 20 pages, 17 figure

Why humans kill animals and why we cannot avoid it

Killing animals has been a ubiquitous human behaviour throughout history, yet it is becoming increasingly controversial and criticised in some parts of contemporary human society. Here we review 10 primary reasons why humans kill animals, discuss the necessity (or not) of these forms of killing, and describe the global ecological context for human killing of animals. Humans historically and currently kill animals either directly or indirectly for the following reasons: (1) wild harvest or food acquisition, (2) human health and safety, (3) agriculture and aquaculture, (4) urbanisation and industrialisation, (5) invasive, overabundant or nuisance wildlife control, (6) threatened species conservation, (7) recreation, sport or entertainment, (8) mercy or compassion, (9) cultural and religious practice, and (10) research,education and testing. While the necessity of some forms of animal killing is debatable and further depends on individual values, we emphasise that several of these forms of animal killing are a necessary component of our inescapable involvement in a single, functioning, finite, global food web. We conclude that humans (and all other animals) cannot live in a way that does not require animal killing either directly or indirectly, but humans can modify some of these killing behaviours in ways that improve the welfare of animals while they are alive, or to reduce animal suffering whenever they must be killed. We encourage a constructive dialogue that (1) accepts and permits human participation in one enormous global food web dependent on animal killing and (2) focuses on animal welfare and environmental sustainability. Doing so will improve the lives of both wild and domestic animals to a greater extent than efforts to avoid, prohibit or vilify human animal-killing behaviour. Animal ethics Conservation biology Culling Factory farmingpublishedVersio