Cache coherence strategies in a many-core processor

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 53-55).Caches are frequently employed in memory systems, exploiting memory locality to gain advantages in high-speed performance and low latency. However, as computer processor core counts increase, maintaining coherence between caches becomes increasingly difficult. Current methods of cache coherence work well in small-scale multi-core processors, however, the viability of cache coherence as processors scale to thousands of cores remains an open question. A novel many-core execution-driven performance simulator, called Graphite and implemented by the Carbon group, has been utilized to study a variety of cache coherency strategies of processors up to 256 cores. Results suggest that cache coherence may be possible in future many-core processors, but that software developers will have to exercise great care to match their algorithms to the target architecture to avoid sub-optimal performance.by Christopher P. Celio.M.Eng

Rigorous Born Approximation and beyond for the Spin-Boson Model

Within the lowest-order Born approximation, we present an exact calculation of the time dynamics of the spin-boson model in the ohmic regime. We observe non-Markovian effects at zero temperature that scale with the system-bath coupling strength and cause qualitative changes in the evolution of coherence at intermediate times of order of the oscillation period. These changes could significantly affect the performance of these systems as qubits. In the biased case, we find a prompt loss of coherence at these intermediate times, whose decay rate is set by $\sqrt{\alpha}$, where $\alpha$ is the coupling strength to the environment. We also explore the calculation of the next order Born approximation: we show that, at the expense of very large computational complexity, interesting physical quantities can be rigorously computed at fourth order using computer algebra, presented completely in an accompanying Mathematica file. We compute the $O(\alpha)$ corrections to the long time behavior of the system density matrix; the result is identical to the reduced density matrix of the equilibrium state to the same order in $\alpha$. All these calculations indicate precision experimental tests that could confirm or refute the validity of the spin-boson model in a variety of systems.Comment: Greatly extended version of short paper cond-mat/0304118. Accompanying Mathematica notebook fop5.nb, available in Source, is an essential part of this work; it gives full details of the fourth-order Born calculation summarized in the text. fop5.nb is prepared in arXiv style (available from Wolfram Research

Microfluidic flow injection immunoassay system for algal toxins determination: a case of study

A novel flow injection microfluidic immunoassay system for continuous monitoring of saxitoxin, a lethal biotoxin, in seawater samples is presented in this article. The system consists of a preimmobilized G protein immunoaffinity column connected in line with a lab-on-chip setup. The detection of saxitoxin in seawater was carried out in two steps: an offline incubation step (competition reaction) performed between the analyte of interest (saxitoxin or Ag, as standard or seawater sample) and a tracer (an enzyme-conjugated antigen or Ag*) toward a specific polyclonal antibody. Then, the mixture was injected through a "loop" of a few mu L using a six-way injection valve into a bioreactor, in line with the valve. The bioreactor consisted of a small glass column, manually filled with resin upon which G protein has been immobilized. When the mixture flowed through the bioreactor, all the antibody-antigen complex, formed during the competition step, is retained by the G protein. The tracer molecules that do not interact with the capture antibody and protein G are eluted out of the column, collected, and mixed with an enzymatic substrate directly within the microfluidic chip, via the use of two peristaltic pumps. When Ag* was present, a color change (absorbance variation, Delta Abs) of the solution is detected at a fixed wavelength (655 nm) by an optical chip docking system and registered by a computer. The amount of saxitoxin, present in the sample (or standard), that generates the variation of the intensity of the color, will be directly proportional to the concentration of the analyte in the analyzed solution. Indeed, the absorbance response increased proportionally to the enzymatic product and to the concentration of saxitoxin in the range of 3.5 x 10(-7)-2 x 10(-5) ng ml(-1) with a detection limit of 1 x 10(-7) ng ml(-1) (RSD% 15, S N-1 equal to 3). The immunoanalytical system has been characterized, optimized, and tested with seawater samples. This analytical approach, combined with the transportable and small-sized instrumentation, allows for easy in situ monitoring of marine water contaminations

Seasonal response of benthic foraminifera to anthropogenic pressure in two stations of the Gulf of Trieste (northern Adriatic Sea, Italy): the marine protected area of Miramare versus the Servola water sewage outfall

A seasonal survey of living benthic foraminifera was performed in 2013 in the Gulf of Trieste (N Adriatic Sea) to compare two marine coastal sites with different degrees of anthropogenic influence. An assessment of ecological quality statuses showed that the station located near the end of an urban pipeline (Ser station), has worse ecological conditions than the site located in a protected marine area (Res station) all year around. Stressed conditions at Ser station were mainly related to high contents of total organic carbon (TOC) and Zn in the bioavailable fraction, which were a limiting factor for the studied foraminiferal communities. Ammonia tepida, Bolivina spp., and Bulimina spp., which characterised this station, were the most tolerant taxa of the studied assemblage. Conversely, Elphidium spp., H. depressula, N. iridea, Quiqueloculina spp., R. nana and Textularia spp., could be considered less tolerant species as they benefitted from the less stressful conditions recorded at Res station, despite slightly higher concentrations of some potentially toxic elements (PTEs), especially Pb, being recorded in this station in comparison to Ser station. Furthermore, foraminiferal assemblages were found to be quite resilient over an annual cycle, being able to recover from a seasonal unbalanced state to a mature one. The beginning of spring and latest summer would be the best period to assess the ecological quality status to avoid any under- or overestimation of the health of the environment

Madera enigmática y primera evidencia de tetrápodos en Formación Yaguarí (Pérmico medio-superior), Uruguay

This article describes an intriguing fossil material recently found in the fine-grained sandstone levels from the upper section of the Yaguarí Formation of Uruguay. The nature of this specimen and its relationships were, initially, not easy to determine with confidence although it was subjected to several analyses, such as morphological and comparative examination complemented with preparation of thin sections and microanatomical and chemical studies under SEM. However, the anatomical structure shown in the performed transversal thin sections allowed solving the issue on the different animal or plant interpretations of the fossil specimen, which was finally discerned in favor of the latter. Therefore, after a detailed comparative study of the thin sections, we concluded that the specimen is a wood fragment related to the Dadoxylon-Araucarioxylon complex. Moreover, in order to provide a better biostratigraphic calibration for these deposits until now devoid of fossils, we include a preliminary description of recently found fossil footprints, which represent the first evidence of the presence of tetrapods in levels of the Yaguarí Formation (sensu Elizalde et al., 1970), below the conglomerates that have yielded the Colonia Orozco Fauna. The footprints were preliminary assigned to the ichnotaxa cf. Karoopes isp, cf. Capitosauroides isp., and cf. Pachypes isp., suggesting the presence of gorgonopsids and therocephalian therapsids and pareiasauromorphs, respectively. The Middle-Late Permian age recently suggested for the Yaguarí Formation based on paleomagnetic and radioisotopic studies is here supported by the described fossils, which thus constitute preliminary but nonetheless relevant discoveries for deposits whose fossiliferous potential has yet to be explored.Este artículo describe un intrigante fósil recientemente descubierto en niveles de areniscas finas a medias de la sección superior de la Formación Yaguarí de Uruguay. La naturaleza y las afinidades de este espécimen no fueron inicialmente fáciles de determinar, a pesar de ser sometido a numerosos estudios, incluido un análisis anatómico-comparativo complementado con la preparación de secciones delgadas y análisis de su microestructura bajo Microscopio Electrónico de Barrido. La microestructura mostrada por las láminas delgadas en corte transversal permitió finalmente resolver el problema sobre discernir entre una naturaleza animal o vegetal del espécimen, siendo la última la aceptada. El detallado estudio comparativo de las secciones delgadas reveló que el espécimen es un fragmento de madera relacionado al complejo Dadoxylon-Araucarioxylon. Asimismo, para proveer una mejor calibración temporal de los depósitos de la sección superior de la Formación Yaguarí (Miembro Villa Viñoles), también se incluye en este trabajo una descripción preliminar de huellas de tetrápodos recientemente halladas en esta unidad, las cuales representan la primera evidencia de la presencia de tetrápodos en niveles de la Formación Yaguarí (sensu Elizalde et al., 1970) subyacentes a los conglomerados portadores de la Fauna de Colonia Orozco. Las huellas fueron asignadas a los icnotaxa cf. Karoopes isp., cf. Capitosauroides isp. y cf. Pachypes isp., sugiriendo la presencia de terápsidos gorgonópsidos y therocefalidos y de pareiasauromorfos, respectivamente. La edad Pérmico Medio a Tardío recientemente sugerida para la Formación Yaguarí, basado en estudios de paleomagnetismo sustentados por dataciones radioisotópicas, es congruente con la aportada por los fósiles aquí descriptos, que, aunque fragmentarios, constituyen descubrimientos preliminarmente relevantes para depósitos cuyo potencial fosilífero no ha sido aún explorado.CSIC: I+D 2016_24

Measurement of the tensor Ayy and vector Ay analyzing powers of the deuteron inelastic scattering off berillium at 5.0 GeV/c and 178 mr

Tensor Ayy and vector Ay analyzing powers in the inelastic scattering of deuterons with the momentum of 5.0 GeV/c on beryllium at an angle of 178 mr in the vicinity of the excitation of baryonic resonances with masses up to 1.8 GeV/c^2 have been measured. The Ayy data are in a good agreement with the previous data obtained at 4.5 and 5.5 GeV/c. The results of the experiment are compared with the predictions of the plane wave impulse approximation and \omega-meson exchange models.Comment: 18 pages, 9 figure

Quantum Computation with Quantum Dots

We propose a new implementation of a universal set of one- and two-qubit gates for quantum computation using the spin states of coupled single-electron quantum dots. Desired operations are effected by the gating of the tunneling barrier between neighboring dots. Several measures of the gate quality are computed within a newly derived spin master equation incorporating decoherence caused by a prototypical magnetic environment. Dot-array experiments which would provide an initial demonstration of the desired non-equilibrium spin dynamics are proposed.Comment: 12 pages, Latex, 2 ps figures. v2: 20 pages (very minor corrections, substantial expansion), submitted to Phys. Rev.

Tissue distribution of DNA-Hsp65/TDM-loaded PLGA microspheres and uptake by phagocytic cells

This study aimed to demonstrate that microspheres, used as delivery vehicle of DNA-Hsp65/TDM [plasmid DNA encoding heat shock protein 65 (Hsp65) coencapsulated with trehalose dimycolate (TDM) into PLGA microspheres], are widely spread among several organs after intramuscular administration in BALB/c mice. In general, we showed that these particles were phagocytosed by antigen presenting cells, such as macrophages and dendritic cells. Besides, it was demonstrated herein that draining lymph node cells presented a significant increase in the number of cells expressing costimulatory molecules (CD80 and CD86) and MHC class II, and also that the administration of the DNA-Hsp65/TDM and vector/TDM formulations resulted in the up-regulation of CD80, CD86 and MHC class II expression when compared to control formulations (vector/TDM and empty). Regarding the intracellular trafficking we observed that following phagocytosis, the microspheres were not found in the late endosomes and/or lysosomes, until 15 days after internalization, and we suggest that these constructions were hydrolysed in early compartments. Overall, these data expand our knowledge on PLGA [poly (lactic-co- glycolic acid)] microspheres as gene carriers in vaccination strategies, as well as open perspectives for their potential use in clinical practice

The problem of equilibration and the computation of correlation functions on a quantum computer

We address the question of how a quantum computer can be used to simulate experiments on quantum systems in thermal equilibrium. We present two approaches for the preparation of the equilibrium state on a quantum computer. For both approaches, we show that the output state of the algorithm, after long enough time, is the desired equilibrium. We present a numerical analysis of one of these approaches for small systems. We show how equilibrium (time)-correlation functions can be efficiently estimated on a quantum computer, given a preparation of the equilibrium state. The quantum algorithms that we present are hard to simulate on a classical computer. This indicates that they could provide an exponential speedup over what can be achieved with a classical device.Comment: 25 pages LaTex + 8 figures; various additional comments, results and correction