RGA users manual : version 2.3

RGA is an interpreter for a special language designed for the analysis of reachability graphs, or control flow graphs, generated from Petri nets. Although in some cases the reachability graph can become too large to be tractable, or can even be infinite, many interesting problems exist whose reachability graphs are of reasonable size. In RGA, the user has access to the names of the places in the net, and to the states of the reachability graph. The structure of the graph is also available through functions which return the sets of successor or predecessor states of a state and the transition-firings connecting the states. The RGA language allows dynamic typing of identifiers, recursion, and function and operator overloading. Rather than providing a number of predefined analysis functions, RGA provides primitive functions which allow the user to conduct complex analyses with little programming effort. RGA is part of a suite of tools, called P-NUT, intended to facilitate the analysis of concurrent systems described by Petri nets

Lagrangian correspondences and Donaldson's TQFT construction of the Seiberg-Witten invariants of 3-manifolds

Using Morse-Bott techniques adapted to the gauge-theoretic setting, we show that the limiting boundary values of the space of finite energy monopoles on a connected 3-manifold with at least two cylindrical ends provides an immersed Lagrangian submanifold of the vortex moduli space at infinity. By studying the signed intersections of such Lagrangians, we supply the analytic details of Donaldson's TQFT construction of the Seiberg-Witten invariants of a closed 3-manifold.Comment: 43 pages. Revised version. To appear in Algebraic & Geometric Topolog

Computer-aided analysis of concurrent systems

The introduction of concurrency into programs has added to the complexity of the software design process. This is most evident in the design of communications protocols where concurrency is inherent to the behavior of the system. The complexity exhibited by such software systems makes more evident the needs for computer-aided tools for automatically analyzing behavior.The Distributed Systems project at UCI has been developing a suite of tools, based on Petri nets, which support the design and evaluation of concurrent software systems. This paper focuses attention on one of the tools: the reachability graph analyzer (RGA). This tool provides mechanisms for proving general system properties (e.g., deadlock-freeness) as well as system-specific properties. The tool is sufficiently general to allow a user to apply complex user-defined analysis algorithms to reachability graphs. The alternating-bit protocol with a bounded channel is used to demonstrate the power of the tool and to point to future extensions

The effect of inflammation on Shiga toxin absorption in vivo

Hemolytic Uremic Syndrome (HUS), the leading cause of acute renal failure in children in the United States, is a systemic complication of Enterohemorrhagic Escherichia coli (EHEC) infection that is caused by the systemic effects of Shiga toxins (Stx) produced by EHEC. Every year approximately 70,000 people in the United States are infected with EHEC, and up to 10% go on to develop HUS. Although it is known that Stx causes HUS, the mechanism of Stx translocation from the intestinal lumen to the systemic circulation is poorly understood. In vitro studies have shown that migration of neutrophils across polarized mucosal epithelial cells enhances the translocation of Stx, but it is not known if a similar phenomenon occurs in vivo. This dissertation tests the hypothesis that the host inflammatory response allows or enhances the translocation of Stx from the intestinal lumen to the systemic circulation. To test the hypothesis, we developed a 3-day-old pig model of EHEC infection using E. coli O157:H7. Colostrum fed neonatal pigs infected with E. coli O15T:H7 at 3 days of age, were colonized by E. coli O157:H7 and developed typical attaching and effacing (A/E) lesions, but lacked a histologically detectable inflammatory response and systemic signs and lesions of Stx toxicosis. In the second set of experiments, we induced inflammation in the cecum, spiral colon, and rectum of neonatal pigs using dextran sulfate sodium (DSS). In the final set of experiments, we compared clinical signs and systemic lesions of Stx toxicosis in pigs infected with E. coli O157:H7 with and without a large intestinal inflammatory response, and in pigs orally dosed with crude Stx preparation with and without a large intestinal inflammatory response. We found that severe suppurative and ulcerative inflammation in the large intestine does not enhance Stx translocation from the intestinal lumen to the systemic circulation in vivo. Further work needs to be done to determine the effect of less severe inflammatory changes on Stx translocation

Characterization of multiphase flows integrating X-ray imaging and virtual reality

Multiphase flows are used in a wide variety of industries, from energy production to pharmaceutical manufacturing. However, because of the complexity of the flows and difficulty measuring them, it is challenging to characterize the phenomena inside a multiphase flow. To help overcome this challenge, researchers have used numerous types of noninvasive measurement techniques to record the phenomena that occur inside the flow. One technique that has shown much success is X-ray imaging. While capable of high spatial resolutions, X-ray imaging generally has poor temporal resolution. This research improves the characterization of multiphase flows in three ways. First, an X-ray image intensifier is modified to use a high-speed camera to push the temporal limits of what is possible with current tube source X-ray imaging technology. Using this system, sample flows were imaged at 1000 frames per second without a reduction in spatial resolution. Next, the sensitivity of X-ray computed tomography (CT) measurements to changes in acquisition parameters is analyzed. While in theory CT measurements should be stable over a range of acquisition parameters, previous research has indicated otherwise. The analysis of this sensitivity shows that, while raw CT values are strongly affected by changes to acquisition parameters, if proper calibration techniques are used, acquisition parameters do not significantly influence the results for multiphase flow imaging. Finally, two algorithms are analyzed for their suitability to reconstruct an approximate tomographic slice from only two X-ray projections. These algorithms increase the spatial error in the measurement, as compared to traditional CT; however, they allow for very high temporal resolutions for 3D imaging. The only limit on the speed of this measurement technique is the image intensifier-camera setup, which was shown to be capable of imaging at a rate of at least 1000 FPS. While advances in measurement techniques for multiphase flows are one part of improving multiphase flow characterization, the challenge extends beyond measurement techniques. For improved measurement techniques to be useful, the data must be accessible to scientists in a way that maximizes the comprehension of the phenomena. To this end, this work also presents a system for using the Microsoft Kinect sensor to provide natural, non-contact interaction with multiphase flow data. Furthermore, this system is constructed so that it is trivial to add natural, non-contact interaction to immersive visualization applications. Therefore, multiple visualization applications can be built that are optimized to specific types of data, but all leverage the same natural interaction. Finally, the research is concluded by proposing a system that integrates the improved X-ray measurements, with the Kinect interaction system, and a CAVE automatic virtual environment (CAVE) to present scientists with the multiphase flow measurements in an intuitive and inherently three-dimensional manner

Reusable Software Technology

The objective of the Reusable Software System (RSS) is to provide NASA Langley Research Center and its contractor personnel with a reusable software technology through the Internet. The RSS is easily accessible, provides information that is extractable, and the capability to submit information or data for the purpose of scientific research at NASA Langley Research Center within the Atmospheric Science Division

The synthesis of cobalt(I) σ-alkane complex and pincer complex catalysts for the generation of polyaminoborane on scale

This thesis at looks the synthesis of a Co(I) σ-alkane complex and the development of cobalt and rhodium catalysts for the dehydropolymerisation of amine-boranes. Chapter 1 provides a brief introduction to the organometallic chemistry of cobalt and rhodium. Chapter 2 describes the synthesis of an X-ray crystallographically characterised cobalt σalkane complex, [Co(Cy2P(CH2)4PCy2)(norbornane)][BArF4]. This complex was prepared by a solid/gas route from a norbornadiene precursor via a single-crystal to single-crystal hydrogenation. SQUID magnetometry data show this complex to be in a triplet electronic state, suggesting this is a relatively unstable σ-alkane complex. Periodic DFT and electronic structure calculations demonstrated the importance of dispersive interactions between the alkane ligand and the anion framework in stabilising weak C-H→Co σ-interactions. In Chapter 3, the simple Co(II) catalyst, Co(NH((CH2)2PiPr2)2)Cl2, was used in amine-borane dehydropolymerisation. This pre-catalyst operates at low loadings to selectively give (H2B·NMeH)n polymer on a 10 g scale. Increasing catalyst loading decreased the Mn of isolated polymer, while maintaining narrow dispersities. A Mayo analysis of the polymer formed and chain transfer agents enabled the speciation of catalysis to be probed. Chapter 4 reports on a bench stable pre-catalyst, [Rh(NH((CH2)2PiPr2)2)NBD]Cl, for the selective dehydropolymerisation of H3B·NMeH2 on 10 g scale. Detailed speciation studies showed an amine-borane adduct Rh(NH((CH2)2Pi Pr2)2)H3(H3B·NMeH2) was the on-cycle resting state. Kinetic profiles of dehydrogenation were determined from eudiometer data and the rate law found to be rate = k[Catalyst]1[H3B·NMeH2]0. Kinetic isotope effects were determined using D3B·NMeH2 and H3B·NMeD2. All these data together with computational studies enabled a catalytic cycle to be determined. Mn could be selectively decreased by doping with [(H2NMe)2BH2]Cl allowing chain control as described by a Mayo analysis. Chapter 3 and 4 have enabled the preparation of polyaminoboranes on scale with chain length control

Self-Assembled Barium Titanate Nanoscale Films by Molecular Beam Epitaxy

One challenge of investigating ferroelectrics at the nanoscale has been controlling the stoichiometry during growth. Historically, the growth of barium titanate (BaTiO3) by molecular beam epitaxy has relied on a growth technique called shuttered RHEED. Shuttered RHEED controls the stoichiometry of barium titanate through the precise deposition of alternating layers of BaO and TiO2. While this approach has achieved 1% control of stoichiometry, finding self-limiting mechanisms to lock-in stoichiometry has been the focus of the growth community. The Goldschmidt tolerance factor predicts an unstable perovskite when barium sits in the titanium lattice site. The BaO-TiO2 phase diagram predicts a low-solubility (\u3c100 ppm) of excess barium oxide at molecular beam epitaxy (MBE) growth temperatures of 600-800 °C. We show that excess barium provided during MBE growth is a self-limiting mechanism to grow stoichiometric barium titanate thin films. Features in RHEED oscillations were identified for both shuttered RHEED and co-deposition that confirm barium rich growth condition. Barium-rich growth condition was confirmed to lead to bulk BTO values for out-of-plane lattice constant, Ti/Ba ratio, and piezoelectric coefficient for 40 nm thick BTO thin films. Angle-resolved x-ray photoelectron spectroscopy studies show that excess barium accumulates at the surface in the form of a barium-rich surface layer referred to here as BaO. For titanium-rich growth condition, the layer assumed stoichiometric bulk BTO values. The excess barium accumulated at the surface was removed with methanol sonication. Barium titanate thin films were shown to self-assemble when excess barium was provided during co-deposition. A systematic comparison of 5 nm thick BTO films grown comparing the shuttered RHEED and co-deposition growth approaches was performed to prove that excess barium doesn’t incorporate into the film but only as BaO at the surface. Both growth approaches produce identical out-of-plane lattice parameter, Ti/Ba ratio, and piezoelectric coefficients. An enhancement in the d33 for the 5 nm thin films compared to the 40 nm thin films was also observed. The compressive strain on 5 nm thin films enhanced the polarization over fully relaxed 40 nm thin films

Graduate Student Research Symposium #2

An opportunity for graduate students who have received Mershon Graduate Student Research Grants to present their research projects to Mershon faculty affiliates and graduate students. Panelists include: Carolyn Morgan, PhD candidate in Political Science and Timothy Leech, PhD candidate in History.Carolyn will be presenting "Fear and Loathing in the Fatherland: How Xenophobia Affects Immigrant Political Engagement" and Timothy will discuss Crossing the Rubicon: The Establishment of the Continental Army and the Decision to Seek Independence, 1774-1776"