A Coupled Multi-ALU Processing Node for a Highly Parallel Computer

This report describes Processor Coupling, a mechanism for controlling multiple ALUs on a single integrated circuit to exploit both instruction-level and inter-thread parallelism. A compiler statically schedules individual threads to discover available intra-thread instruction-level parallelism. The runtime scheduling mechanism interleaves threads, exploiting inter-thread parallelism to maintain high ALU utilization. ALUs are assigned to threads on a cycle byscycle basis, and several threads can be active concurrently. Simulation results show that Processor Coupling performs well both on single threaded and multi-threaded applications. The experiments address the effects of memory latencies, function unit latencies, and communication bandwidth between function units.

The Coupled Depth/Slope Approach to Surface Reconstruction

Reconstructing a surface from sparse sensory data is a well known problem in computer vision. Early vision modules typically supply sparse depth, orientation and discontinuity information. The surface reconstruction module incorporates these sparse and possibly conflicting measurements of a surface into a consistent, dense depth map. The coupled depth/slope model developed here provides a novel computational solution to the surface reconstruction problem. This method explicitly computes dense slope representation as well as dense depth representations. This marked change from previous surface reconstruction algorithms allows a natural integration of orientation constraints into the surface description, a feature not easily incorporated into earlier algorithms. In addition, the coupled depth/ slope model generalizes to allow for varying amounts of smoothness at different locations on the surface. This computational model helps conceptualize the problem and leads to two possible implementations- analog and digital. The model can be implemented as an electrical or biological analog network since the only computations required at each locally connected node are averages, additions and subtractions. A parallel digital algorithm can be derived by using finite difference approximations. The resulting system of coupled equations can be solved iteratively on a mesh-pf-processors computer, such as the Connection Machine. Furthermore, concurrent multi-grid methods are designed to speed the convergence of this digital algorithm.

On-line concentration of proteins in pressurized capillary electrochromatography coupled with electrospray ionization-mass spectrometry

Pressurized capillary electrochromatography (pCEC) and electrospray ionization-mass spectrometry (ESI-MS) have been hyphenated for protein analysis. Taken cytochrome c, lysozyme, and insulin as samples, the limits of detection (LODs) for absolute concentrations are 10(-11) mol (signal-to-noise ratio S/N = 3) with relative standard deviations (RSDs) of retention time and peak area, respectively, of less than 1.7% and 4.8%. In order to improve the detection sensitivity, on-line concentration by field-enhanced sample-stacking effect and chromatographic zone-sharpening effect has been developed, and parameters affecting separation and detection, such as pH and electrolyte concentration in the mobile phase, separation voltage, as well as enrichment voltage and time, have been studied systematically. Under the optimized conditions, the LODs of the three proteins could be decreased up to 100-fold. In addition, the feasibility of such techniques has been further demonstrated by the analysis of modified insulins at a concentration of 20 mu g/mL.

Determination of urinary nucleosides by direct injection and coupled-column high-performance liquid chromatography

A coupled-column liquid chromatographic method for the direct analysis of 14 urinary nucleosides is described. Efficient on-line clean-up and concentration of 14 nucleosides from urine samples were obtained by using a boronic acid-substituted silica column (40 turn x 4.0 mm I.D.) as the first column (Col-1) and a Hypersil ODS2 column (250 mm x 4.6 mm I.D.) as the second column (Col-2). The mobile phases applied consisted of 0.25 mol/L ammonium acetate (pH 8.5) on Col-1, and of 25 mmol/L potassium dihydrogen phosphate (pH 4.5) on Col-2, respectively. Determination of urinary nucleosides was performed on Col-2 column by using a linear gradient elution comprising 25 mmol/L potassium dihydrogen phosphate (pH 4.5) and methanol-water (60:40, v/v) with UV detection at 260 nm. Urinary nucleosides analysis can be carried out by this procedure in 50 min requiring only pH adjustment and the protein precipitation by centrifugation of urine samples. Calibration plots of 14 standard nucleosides showed excellent linearity (r > 0.995) and the limits of detection were at micromolar levels. Both of intra- and inter-day precisions of the method were better than 6.6% for direct determination of 14 nucleosides. The validated method was applied to quantify 14 nucleosides in 20 normal urines to establish reference ranges. (c) 2005 Elsevier B.V. All rights reserved.

Quantitative determination of compounds in tobacco essential oils by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry

A quantitative analysis of the individual compounds in tobacco essential oils is performed by comprehensive two-dimensional gas chromatography (GC x GC) combined with flame ionization detector (FID). A time-of-flight mass spectrometer (TOF/MS) was coupled to GC x GC for the identification of the resolved peaks. The response of a flame ionization detector to different compound classes was calibrated using multiple internal standards. In total, 172 compounds were identified with good match and 61 compounds with high probability value were reliably quantified. For comparative purposes, the essential oil sample was also quantified by one-dimensional gas chromatography-mass spectrometry (GC/MS) with multiple internal standards method. The results showed that there was close agreement between the two analysis methods when the peak purity and match quality in one-dimensional GC/MS are high enough. (c) 2005 Elsevier B.V. All rights reserved.

Interface of chip-based capillary electrophoresis-inductively coupled plasma-atomic emission spectrometry (CE-ICP-AES)

An interface of chip-based capillary electrophoresis (CE)-inductively coupled plasma-atomic emission spectrometry (ICP-AES) that is based on cross-flow nebulization has been developed. A polydimethylsiloxane (PDMS) CE-chip with conventional cross channel layout was used. A stainless steel tube was placed orthogonal to the exit of the CE separation channel for cross flow nebulization. A supplementary flow of buffer solution at the channel exit was used to improve nebulization efficiency. Two capillaries were inserted into the CE chip near the inlet of the separation channel for sample and buffer solution injection. Syringe pumps were used to manipulate the flow rate and flow direction of the sample, buffer, and supplementary buffer solution. Peak broadening due to the shape (bulb and tube-shaped) and size of the spray chambers was studied. The smaller tube-shaped spray chamber was used because of smaller peak broadening effect due to aerosol transport. The nebulization and transport efficiency of the CE-ICP interface was approximately 10%. Ba2+ and Mg2+ ions were eluted from the CE-chip within 30 s. Resolution of the Ba2+ and Mg2+ peaks was 0.7 using the chip-based CE-ICP-AES system.

ROMA: Reliable Overlay Multicast with Loosely Coupled TCP Connections

We consider the problem of architecting a reliable content delivery system across an overlay network using TCP connections as the transport primitive. We first argue that natural designs based on store-and-forward principles that tightly couple TCP connections at intermediate end-systems impose fundamental performance limitations, such as dragging down all transfer rates in the system to the rate of the slowest receiver. In contrast, the ROMA architecture we propose incorporates the use of loosely coupled TCP connections together with fast forward error correction techniques to deliver a scalable solution that better accommodates a set of heterogeneous receivers. The methods we develop establish chains of TCP connections, whose expected performance we analyze through equation-based methods. We validate our analytical findings and evaluate the performance of our ROMA architecture using a prototype implementation via extensive Internet experimentation across the PlanetLab distributed testbed.

Experimental study of quantum dot and dash lasers

Quantum dashes are elongated quantum dots. Polarized edge-photovoltage and spontaneous emission spectroscopy are used to study the anisotropy of optical properties in 1.5μm InGaAsP and AlGaInAs-based quantum dash lasers. Strain, which causes TM-polarized transitions to be suppressed at the band edge, coupled with carrier confinement and dash shape leads to an enhancement of the optical properties for light polarized along the dash long axis, in excellent agreement with theoretical results. An analysis of the integrated facet and spontaneous emission rate with total current and temperature reveals that, in both undoped and p-doped InGaAsP-based quantum dash lasers at room temperature, the threshold current and its temperature dependence remain dominated by Auger recombination. We also identify two processes which can limit the output power and propose that the effects of the dopant in p-doped InGaAsP-based lasers dominate at low temperature but decrease with increasing temperature. A high threshold current density in undoped AlGaInAs-based quantum dash laser samples studied, which degrade rapidly at low temperature, is not due to intrinsic carrier recombination processes. 1.3μm GaAs-based quantum dots lasers have been widely studied, but there remains issues as to the nature of the electronic structure. Polarized edge-photovoltage spectroscopy is used to investigate the energy distribution and nature of the energy states in InAs/GaAs quantum dot material. A non-negligible TM-polarized transition, which is often neglected in calculations and analyses, is measured close to the main TE-polarized ground state transition. Theory is in very good agreement with the experimental results and indicates that the measured low-energy TM-polarized transition is due to the strong spatial overlap between the ground state electron and the light-hole component of a low-lying excited hole state. Further calculations suggest that the TM-polarized transition reduces at the band edge as the quantum dot aspect ratio decreases.

Hybrid integration and packaging of grating-coupled silicon photonics

This thesis covers both the packaging of silicon photonic devices with fiber inputs and outputs as well as the integration of laser light sources with these same devices. The principal challenge in both of these pursuits is coupling light into the submicrometer waveguides that are the hallmark of silicon-on-insulator (SOI) systems. Previous work on grating couplers is leveraged to design new approaches to bridge the gap between the highly-integrated domain of silicon, the Interconnected world of fiber and the active region of III-V materials. First, a novel process for the planar packaging of grating couplers with fibers is explored in detail. This technology allows the creation of easy-to-use test platforms for laser integration and also stands on its own merits as an enabling technology for next-generation silicon photonics systems. The alignment tolerances of this process are shown to be well-suited to a passive alignment process and for wafer-scale assembly. Furthermore, this technology has already been used to package demonstrators for research partners and is included in the offerings of the ePIXfab silicon photonics foundry and as a design kit for PhoeniX Software’s MaskEngineer product. After this, a process for hybridly integrating a discrete edge-emitting laser with a silicon photonic circuit using near-vertical coupling is developed and characterized. The details of the various steps of the design process are given, including mechanical, thermal, optical and electrical steps. The interrelation of these design domains is also discussed. The construction process for a demonstrator is outlined, and measurements are presented of a series of single-wavelength Fabry-Pérot lasers along with a two-section laser tunable in the telecommunications C-band. The suitability and potential of this technology for mass manufacture is demonstrated, with further opportunities for improvement detailed and discussed in the conclusion.

Development of germanium/silicon integration for near infrared detection

Silicon (Si) is the base material for electronic technologies and is emerging as a very attractive platform for photonic integrated circuits (PICs). PICs allow optical systems to be made more compact with higher performance than discrete optical components. Applications for PICs are in the area of fibre-optic communication, biomedical devices, photovoltaics and imaging. Germanium (Ge), due to its suitable bandgap for telecommunications and its compatibility with Si technology is preferred over III-V compounds as an integrated on-chip detector at near infrared wavelengths. There are two main approaches for Ge/Si integration: through epitaxial growth and through direct wafer bonding. The lattice mismatch of ~4.2% between Ge and Si is the main problem of the former technique which leads to a high density of dislocations while the bond strength and conductivity of the interface are the main challenges of the latter. Both result in trap states which are expected to play a critical role. Understanding the physics of the interface is a key contribution of this thesis. This thesis investigates Ge/Si diodes using these two methods. The effects of interface traps on the static and dynamic performance of Ge/Si avalanche photodetectors have been modelled for the first time. The thesis outlines the original process development and characterization of mesa diodes which were fabricated by transferring a ~700 nm thick layer of p-type Ge onto n-type Si using direct wafer bonding and layer exfoliation. The effects of low temperature annealing on the device performance and on the conductivity of the interface have been investigated. It is shown that the diode ideality factor and the series resistance of the device are reduced after annealing. The carrier transport mechanism is shown to be dominated by generation–recombination before annealing and by direct tunnelling in forward bias and band-to-band tunnelling in reverse bias after annealing. The thesis presents a novel technique to realise photodetectors where one of the substrates is thinned by chemical mechanical polishing (CMP) after bonding the Si-Ge wafers. Based on this technique, Ge/Si detectors with remarkably high responsivities, in excess of 3.5 A/W at 1.55 μm at −2 V, under surface normal illumination have been measured. By performing electrical and optical measurements at various temperatures, the carrier transport through the hetero-interface is analysed by monitoring the Ge band bending from which a detailed band structure of the Ge/Si interface is proposed for the first time. The above unity responsivity of the detectors was explained by light induced potential barrier lowering at the interface. To our knowledge this is the first report of light-gated responsivity for vertically illuminated Ge/Si photodiodes. The wafer bonding approach followed by layer exfoliation or by CMP is a low temperature wafer scale process. In principle, the technique could be extended to other materials such as Ge on GaAs, or Ge on SOI. The unique results reported here are compatible with surface normal illumination and are capable of being integrated with CMOS electronics and readout units in the form of 2D arrays of detectors. One potential future application is a low-cost Si process-compatible near infrared camera.

Two closely coupled lasers, dynamics & applications

The dynamics of two mutually coupled identical single-mode semi-conductor lasers are theoretically investigated. For small separation and large coupling between the lasers, symmetry-broken one-colour states are shown to be stable. In this case the light output of the lasers have significantly different intensities whilst at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable two-colour states, where both single-mode lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. For low coupling but possibly large separation, the frequency of the relaxation oscillations of the freerunning lasers defines the dynamics. Chaotic and quasi-periodic states are identified and shown to be stable. For weak coupling undamped relaxation oscillations dominate where each laser is locked to three or more odd number of colours spaced by the relaxation oscillation frequency. It is shown that the instabilities that lead to these states are directly connected to the two colour mechanism where the change in the number of optical colours due to a change in the plane of oscillation. At initial coupling, in-phase and anti-phase one colour states are shown to emerge from “on” uncoupled lasers using a perturbation method. Similarly symmetry-broken one-colour states come from considering one free-running laser initially “on” and the other laser initially “off”. The mechanism that leads to a bi-stability between in-phase and anti-phase one-colour states is understood. Due to an equivariant phase space symmetry of being able to exchange the identical lasers, a symmetric and symmetry-broken variant of all states mentioned above exists and is shown to be stable. Using a five dimensional model we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-colour, symmetric and symmetry-broken two-colour, symmetric and symmetry-broken undamped relaxation oscillations, symmetric and symmetry-broken quasi-periodic, and symmetric and symmetry-broken chaotic states. As symmetry-broken states always exist in pairs, they naturally give rise to bi-stability. Several of these states show multistabilities between symmetric and symmetry-broken variants and among states. Three memory elements on the basis of bi-stabilities in one and two colour states for two coupled single-mode lasers are proposed. The switching performance of selected designs of optical memory elements is studied numerically.

Reciprocal in vivo regulation of myocardial G protein-coupled receptor kinase expression by beta-adrenergic receptor stimulation and blockade.

BACKGROUND: Impaired myocardial beta-adrenergic receptor (betaAR) signaling, including desensitization and functional uncoupling, is a characteristic of congestive heart failure. A contributing mechanism for this impairment may involve enhanced myocardial beta-adrenergic receptor kinase (betaARK1) activity because levels of this betaAR-desensitizing G protein-coupled receptor kinase (GRK) are increased in heart failure. An hypothesis has emerged that increased sympathetic nervous system activity associated with heart failure might be the initial stimulus for betaAR signaling alterations, including desensitization. We have chronically treated mice with drugs that either activate or antagonize betaARs to study the dynamic relationship between betaAR activation and myocardial levels of betaARK1. METHODS AND RESULTS: Long-term in vivo stimulation of betaARs results in the impairment of cardiac +betaAR signaling and increases the level of expression (mRNA and protein) and activity of +betaARK1 but not that of GRK5, a second GRK abundantly expressed in the myocardium. Long-term beta-blocker treatment, including the use of carvedilol, improves myocardial betaAR signaling and reduces betaARK1 levels in a specific and dose-dependent manner. Identical results were obtained in vitro in cultured cells, demonstrating that the regulation of GRK expression is directly linked to betaAR signaling. CONCLUSIONS: This report demonstrates, for the first time, that betaAR stimulation can significantly increase the expression of betaARK1 , whereas beta-blockade decreases expression. This reciprocal regulation of betaARK1 documents a novel mechanism of ligand-induced betaAR regulation and provides important insights into the potential mechanisms responsible for the effectiveness of beta-blockers, such as carvedilol, in the treatment of heart failure.

Regulation of G protein-coupled receptor signaling by scaffold proteins.

The actions of many hormones and neurotransmitters are mediated through stimulation of G protein-coupled receptors. A primary mechanism by which these receptors exert effects inside the cell is by association with heterotrimeric G proteins, which can activate a wide variety of cellular enzymes and ion channels. G protein-coupled receptors can also interact with a number of cytoplasmic scaffold proteins, which can link the receptors to various signaling intermediates and intracellular effectors. The multicomponent nature of G protein-coupled receptor signaling pathways makes them ideally suited for regulation by scaffold proteins. This review focuses on several specific examples of G protein-coupled receptor-associated scaffolds and the roles they may play in organizing receptor-initiated signaling pathways in the cardiovascular system and other tissues.

The G-protein-coupled receptor kinases beta ARK1 and beta ARK2 are widely distributed at synapses in rat brain.

The beta-adrenergic receptor kinase (beta ARK) phosphorylates the agonist-occupied beta-adrenergic receptor to promote rapid receptor uncoupling from Gs, thereby attenuating adenylyl cyclase activity. Beta ARK-mediated receptor desensitization may reflect a general molecular mechanism operative on many G-protein-coupled receptor systems and, particularly, synaptic neurotransmitter receptors. Two distinct cDNAs encoding beta ARK isozymes were isolated from rat brain and sequenced. The regional and cellular distributions of these two gene products, termed beta ARK1 and beta ARK2, were determined in brain by in situ hybridization and by immunohistochemistry at the light and electron microscopic levels. The beta ARK isozymes were found to be expressed primarily in neurons distributed throughout the CNS. Ultrastructurally, beta ARK1 and beta ARK2 immunoreactivities were present both in association with postsynaptic densities and, presynaptically, with axon terminals. The beta ARK isozymes have a regional and subcellular distribution consistent with a general role in the desensitization of synaptic receptors.