Doctor of Philosophy

dissertationThe study of the reactions of Sm+ and Th+ with several small molecules using guided ion beam tandem mass spectrometry is presented. The kinetic energy dependent reaction cross sections of these reactions are modelled using a modified line-of-centers model, and thermochemical values, including bond dissociation energies (BDEs), are reported. In most cases, the experimental BDEs are compared to BDEs derived from quantum chemical calculations. Furthermore, a semiempirical model to include spin-orbit energy corrections to theoretical calculations is presented. Finally, experimental Th+ BDEs are used to elucidate the thermochemical trends of the actinide series

Regulatory activity revealed by dynamic correlations in gene expression noise

Gene regulatory interactions are context dependent, active in some cellular states but not in others. Stochastic fluctuations, or 'noise', in gene expression propagate through active, but not inactive, regulatory links^(1,2). Thus, correlations in gene expression noise could provide a noninvasive means to probe the activity states of regulatory links. However, global, 'extrinsic', noise sources generate correlations even without direct regulatory links. Here we show that single-cell time-lapse microscopy, by revealing time lags due to regulation, can discriminate between active regulatory connections and extrinsic noise. We demonstrate this principle mathematically, using stochastic modeling, and experimentally, using simple synthetic gene circuits. We then use this approach to analyze dynamic noise correlations in the galactose metabolism genes of Escherichia coli. We find that the CRP-GalS-GalE feed-forward loop is inactive in standard conditions but can become active in a GalR mutant. These results show how noise can help analyze the context dependence of regulatory interactions in endogenous gene circuits

The drag on a microcantilever oscillating near a wall

Motivated by devices such as the atomic force microscope, we compute the drag experienced by a cylindrical body of circular or rectangular cross-section oscillating at small amplitude near a plane wall. The body lies parallel to the wall and oscillates normally to it; the body is assumed to be long enough for the dominant flow to be two-dimensional. The flow is parameterized by a frequency parameter γ² (a Strouhal number) and the wall–body separation Δ (scaled on body radius). Numerical solutions of the unsteady Stokes equations obtained using finite-difference computations in bipolar coordinates (for circular cross-sections) and boundary-element computations (for rectangular cross-sections) are used to determine the drag on the body. Numerical results are validated and extended using asymptotic predictions (for circular cylinders) obtained at all extremes of (γ, Δ)-parameter space. Regions in parameter space for which the wall has a significant effect on drag are identified.R. J. Clarke, S. M. Cox, P. M. Williams and O. E. Jense

A methodology for the capture and analysis of hybrid data: a case study of program debugging

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Stratospheric processes: Observations and interpretation

Explaining the observed ozone trends discussed in an earlier update and predicting future trends requires an understanding of the stratospheric processes that affect ozone. Stratospheric processes occur on both large and small spatial scales and over both long and short periods of time. Because these diverse processes interact with each other, only in rare cases can individual processes be studied by direct observation. Generally the cause and effect relationships for ozone changes were established by comparisons between observations and model simulations. Increasingly, these comparisons rely on the developing, observed relationships among trace gases and dynamical quantities to initialize and constrain the simulations. The goal of this discussion of stratospheric processes is to describe the causes for the observed ozone trends as they are currently understood. At present, we understand with considerable confidence the stratospheric processes responsible for the Antarctic ozone hole but are only beginning to understand the causes of the ozone trends at middle latitudes. Even though the causes of the ozone trends at middle latitudes were not clearly determined, it is likely that they, just as those over Antarctica, involved chlorine and bromine chemistry that was enhanced by heterogeneous processes. This discussion generally presents only an update of the observations that have occurred for stratospheric processes since the last assessment (World Meteorological Organization (WMO), 1990), and is not a complete review of all the new information about stratospheric processes. It begins with an update of the previous assessment of polar stratospheres (WMO, 1990), followed by a discussion on the possible causes for the ozone trends at middle latitudes and on the effects of bromine and of volcanoes

Crossing the Communication Chasm: Challenges and Opportunities in Transitions of Care from the Hospital to the Primary Care Clinic

Background Transitions of care from specialty and acute settings to primary care abound. Compared to the continuity in end-of-shift handoffs, care transitions involve provider communication between practices and facilities with their own cultures and bureaucracies. Using the transition from acute care to outpatient primary care for stroke/transient ischemic attack (TIA) patients as a case study, this qualitative research explored communication practices and institutional arrangements among clinical providers responsible for longitudinal management of hypertension. In this study, researchers investigated the barriers and facilitators of effective communication between acute stroke/TIA inpatient and primary care providers at a Veterans Affairs Medical Center. Methods A multidisciplinary team conducted consensus-based coding and thematic analysis of semistructured interviews with 21 clinical providers (9 with primary responsibilities for inpatient care and 12 with primary responsibilities in outpatient, primary care). Results Thematic analysis of responses identified three factors that influenced communication between clinical providers: (1) consistent, concise but complete medication and treatment plans; (2) reliable, standardized discharge documentation; (3) use of multiple modes of communication. Participants identified cultural barriers, including challenges with rotating providers at a teaching hospital and local discharge practices. Conclusion Ambiguity about who is being handed off to and time pressures in the acute setting may lead inpatient providers to give lower priority to discharge communication, leaving outpatient providers with low-quality information. While electronic templates have standardized key components of discharge documentation, improvement opportunities remain. Increased awareness of the challenges and opportunities on each side of the care transfer could foster communication practices that systematically account for the information needs of inpatient and outpatient providers

Helioseismology can test the Maxwell-Boltzmann distribution

Nuclear reactions in stars occur between nuclei in the high-energy tail of the energy distribution and are sensitive to possible deviations from the standard equilibrium thermal-energy distribution. We are able to derive strong constraints on such deviations by using the detailed helioseismic information of the solar structure. If a small deviation is parameterized with a factor exp{-delta*(E/kT)^2}, we find that delta should lie between -0.005 and +0.002. However, even values of delta as small as 0.003 would still give important effects on the neutrino fluxes.Comment: 10 pages in ReVTeX + 1 postscript figure. Submitted to Phys. Lett.

Magnetic field tunable vortex diode made of YBa2Cu3O7−δ Josephson junction asymmetrical arrays

Several Josephson ratchets designed as asymmetrically structured parallel-series arrays of Josephson junctions made of YBa2Cu3O7−δ have been fabricated. From the current-voltage characteristics measured for various values of applied magnetic field, B, in the temperature range of 10–89 K, we demonstrate that the devices work as magnetic field-tunable highly reversible vortex diodes. Thus, at 89 K, the ratchet efficiency η could be reversed from +60% to −60% with a change in B as small as 3 μT. By decreasing the operation temperature, η improves up to −95% at 10 K while the dynamics in the B-tunability degrades. The ratchet designs we propose here can be used to control unidirectional vortex flow vortices in superconducting devices as well as building integrated nano-magnetic sensors. Numerical simulations qualitatively confirm our experimental findings and also provide insight into the related and more general problem of the control of the transport of nano/quantum objects in thin films

Yours ever (well, maybe): Studies and signposts in letter writing

Electronic mail and other digital communications technologies seemingly threaten to end the era of handwritten and typed letters, now affectionately seen as part of snail mail. In this essay, I analyze a group of popular and scholarly studies about letter writing-including examples of pundits critiquing the use of e-mail, etiquette manuals advising why the handwritten letter still possesses value, historians and literary scholars studying the role of letters in the past and what it tells us about our present attitudes about digital communications technologies, and futurists predicting how we will function as personal archivists maintaining every document including e-mail. These are useful guideposts for archivists, providing both a sense of the present and the past in the role, value and nature of letters and their successors. They also provide insights into how such documents should be studied, expanding our gaze beyond the particular letters, to the tools used to create them and the traditions dictating their form and function. We also can discern a role for archivists, both for contributing to the literature about documents and in using these studies and commentaries, suggesting not a new disciplinary realm but opportunities for new interdisciplinary work. Examining a documentary form makes us more sensitive to both the innovations and traditions as it shifts from the analog to the digital; we can learn not to be caught up in hysteria or nostalgia about one form over another and archivists can learn about what they might expect in their labors to document society and its institutions. At one time, paper was part of an innovative technology, with roles very similar to the Internet and e-mail today. It may be that the shifts are far less revolutionary than is often assumed. Reading such works also suggests, finally, that archivists ought to rethink how they view their own knowledge and how it is constructed and used. © 2010 Springer Science+Business Media B.V