Publications

A Brain-Emulating Cognition and Control Architecture (BECCA) is presented. It is consistent with the hypothesized functions of pervasive intra-cortical and cortico-subcortical neural circuits. It is able to reproduce many salient aspects of human voluntary movement and motor learning. It also provides plausible mechanisms for many phenomena described in cognitive psychology, including perception and mental modeling. Both "inputs" (afferent channels) and "outputs"' (efferent channels) are treated as neural signals; they are all binary (either on or off) and there is no meaning, information, or tag associated with any of them. Although BECCA initially has no internal models, it learns complex interrelations between outputs and inputs through which it bootstraps a model of the system it is controlling and the outside world. BECCA uses two key algorithms to accomplish this: S-Learning and Context-Based Similarity (CBS).

We describe a novel approach to fabricate high-aspect-ratio membranes in microchannels by direct laser scanning, and demonstrate >10-fold improvement in sample preconcentration speed by achieving lower fM detection of proteins within 5 minutes. The integrated device can be used for continuous sample preparation, injection, preconcentration, and biochemical binding/reaction applications. © 2008 CBMS.

Abstract not provided.

A sub-scale experiment has been constructed using fins mounted on one wall of a transonic wind tunnel to investigate the influence of fin trailing vortices upon downstream control surfaces. Data are collected using a fin balance instrumenting the downstream fin to measure the aerodynamic forces of the interaction, combined with stereoscopic Particle Image Velocimetry to determine vortex properties. The fin balance data show that the response of the downstream fin essentially is shifted from the baseline single-fin data dependent upon the angle of attack of the upstream fin. Freestream Mach number and the spacing between fins have secondary effects. The velocimetry shows that the vortex strength increases markedly with upstream fin angle of attack, though even an uncanted fin generates a noticeable wake. No variation with Mach number can be discerned in the normalized velocity data. Correlations between the force data and the velocimetry suggest that the interaction is fundamentally a result of an angle of attack superposed upon the downstream fin by the vortex shed from the upstream fin tip. The Mach number influence arises from differing vortex lift on the leading edge of the downstream fin even when the impinging vortex is Mach invariant.

Abstract not provided.

Abstract not provided.

An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in addressing real-world "wickedly difficult" challenges. Previous laboratory research has engaged small groups of students in answering questions irrelevant to an industrial setting. The current experiment extended this research to larger, real-world employee groups engaged in addressing organizationrelevant challenges. Within the present experiment, the data demonstrated that individuals performed at least as well as groups in terms of number of ideas produced and significantly (p<.02) outperformed groups in terms of the quality of those ideas (as measured along the dimensions of originality, feasibility, and effectiveness).

Latent Semantic Analysis (LSA) is based on the Singular Value Decomposition (SVD) of a term-by-document matrix for identifying relationships among terms and documents from cooccurrence patterns. Among the multiple ways of computing the SVD of a rectangular matrix X, one approach is to compute the eigenvalue decomposition (EVD) of a square 2 × 2 composite matrix consisting of four blocks with X and XT in the off-diagonal blocks and zero matrices in the diagonal blocks. We point out that significant value can be added to LSA by filling in some of the values in the diagonal blocks (corresponding to explicit term-to-term or document-to-document associations) and computing a term-by-concept matrix from the EVD. For the case of multilingual LSA, we incorporate information on cross-language term alignments of the same sort used in Statistical Machine Translation (SMT). Since all elements of the proposed EVD-based approach can rely entirely on lexical statistics, hardly any price is paid for the improved empirical results. In particular, the approach, like LSA or SMT, can still be generalized to virtually any language(s); computation of the EVD takes similar resources to that of the SVD since all the blocks are sparse; and the results of EVD are just as economical as those of SVD. © 2008 Licensed under the Creative Commons.

Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), is a growing international health crisis. Mtb is able to persist in host tissues in a nonreplicating persistent (NRP) or latent state. This presents a challenge in the treatment of TB. Latent TB can re-activate in 10% of individuals with normal immune systems, higher for those with compromised immune systems. A quantitative understanding of latency-associated virulence mechanisms may help researchers develop more effective methods to battle the spread and reduce TB associated fatalities. Leveraging BioXyce's ability to simulate whole-cell and multi-cellular systems we are developing a circuit-based framework to investigate the impact of pathogenicity-associated pathways on the latency/reactivation phase of tuberculosis infection. We discuss efforts to simulate metabolic pathways that potentially impact the ability of Mtb to persist within host immune cells. We demonstrate how simulation studies can provide insight regarding the efficacy of potential anti-TB agents on biological networks critical to Mtb pathogenicity using a systems chemical biology approach. © 2008 IEEE.

Abstract not provided.

We develop an approach for estimating model parameters which result in the "best distribution fit" between experimental and simulation data. Best distribution fit means matching moments of experimental data to those of a simulation (and possibly matching a full probability distribution). This approach extends typical nonlinear least squares methods which identify parameters maximizing agreement between experimental points and computational simulation results. Several analytic formulations for the distribution matching problem are provided, along with results for solving test problems and comparisons of this parameter estimation technique with a deterministic least squares approach. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc.

We describe a novel approach to fabricate high-aspect-ratio membranes in microchannels by direct laser scanning, and demonstrate >10-fold improvement in sample preconcentration speed by achieving lower fM detection of proteins within 5 minutes. The integrated device can be used for continuous sample preparation, injection, preconcentration, and biochemical binding/reaction applications. © 2008 CBMS.

The rich history of scalable computing research owes much to a rapid rise in computing platform scale in terms of size and speed. As platforms evolve, so must algorithms and the software expressions of those algorithms. Unbridled growth in scale inevitably leads to complexity. This special issue grapples with two facets of this complexity: scalable execution and scalable development. The former results from efficient programming of novel hardware with increasing numbers of processing units (e.g., cores, processors, threads or processes). The latter results from efficient development of robust, flexible software with increasing numbers of programming units (e.g., procedures, classes, components or developers). The progression in the above two parenthetical lists goes from the lowest levels of abstraction (hardware) to the highest (people). This issue's theme encompasses this entire spectrum. The lead author of each article resides in the Scalable Computing Research and Development Department at Sandia National Laboratories in Livermore, CA. Their co-authors hail from other parts of Sandia, other national laboratories and academia. Their research sponsors include several programs within the Department of Energy's Office of Advanced Scientific Computing Research and its National Nuclear Security Administration, along with Sandia's Laboratory Directed Research and Development program and the Office of Naval Research. The breadth of interests of these authors and their customers reflects in the breadth of applications this issue covers. This article demonstrates how to obtain scalable execution on the increasingly dominant high-performance computing platform: a Linux cluster with multicore chips. The authors describe how deep memory hierarchies necessitate reducing communication overhead by using threads to exploit shared register and cache memory. On a matrix-matrix multiplication problem, they achieve up to 96% parallel efficiency with a three-part strategy: intra-node multithreading, non-blocking inter-node message passing, and a dedicated communications thread to facilitate concurrent communications and computations. On a quantum chemistry problem, they spawn multiple computation threads and communication threads on each node and use one-sided communications between nodes to minimize wait times. They reduce software complexity by evolving a multi-threaded factory pattern in C++ from a working, message-passing program in C.

Reaction dynamics in exothermic Co/Al multilayer foils are studied with high speed digital photography. Unsteady, spin-like reaction propagation is observed in which the net synthesis of a foil is accomplished through advancing transverse bands that propagate perpendicular to the net reaction direction. This unsteady behavior is connected to the final reacted foil surface morphology that exhibits periodic structures. The evolution of the reaction front shape and corresponding surface morphology are discussed with respect to Co/Al foil characteristics. © 2009 Materials Research Society.

The monolithic nature of transportation technologies offers opportunities for significant improvements in efficiency of 25-50% through strategic technical investments in both advanced fuels and new low-temperature engine concepts. The application of direct numerical simulation (DNS) provides a way to study fundamental issues related to small-scale combustion processes in well-defined canonical configurations, whereas the application of large eddy simulation (LES) provides a formal treatment of the full range of time and length scales that exist in turbulent reacting flows, and thus provides a direct link to experimental studies of relevant combustion devices. In the present study, through DOE INCITE and Oak Ridge National Laboratory 250 Tflop Transition-to-Operations grants in 2008, DNS is performed to understand how a lifted autoignitive flame is stabilized, and LES is performed to understand the high-pressure injection and mixing processes in internal combustion engines. Understanding of these and other fundamental issues is needed to develop robust and reliable ignition and combustion models for the combustion regimes observed under low-temperature combustion engine environments using alternative fuels. © 2008 IOP Publishing Ltd.

A coupled Euler-Lagrange solution approach is used to model the response of a buried reinforced concrete structure subjected to a close-in detonation of a high explosive charge. The coupling algorithm is discussed along with a set of benchmark calculations involving detonations in clay and sand.

The disturbed rock zone constitutes an important geomechanical element of the Waste Isolation Pilot Plant. The science and engineering underpinning the disturbed rock zone provide the basis for evaluating ongoing operational issues and their impact on performance assessment. Contemporary treatment of the disturbed rock zone applied to the evaluation of the panel closure system and to a new mining horizon improves the level of detail and quantitative elements associated with a damaged zone surrounding the repository openings. Technical advancement has been realized by virtue of ongoing experimental investigations and international collaboration. Initial sections summarize and document theoretical and experimental results, which quantify characteristics of the disturbed rock zone as applied to nuclear waste repositories in salt. This information is then applied to operational issues pertaining to recertification of the repository. © 2008 ASCE.

A total system performance assessment (TSPA) model has been developed to analyze the ability of the natural and engineered barriers of the Yucca Mountain repository to isolate nuclear waste over the period following repository closure. The principal features of the engineered barrier system are emplacement tunnels (or "drifts") containing a two-layer waste package (WP) for waste containment and a titanium drip shield to protect the WP from seeping water and falling rock. The 25-mm-thick outer shell of the WP is composed of Alloy 22, a highly corrosion-resistant nickel-based alloy. There are five nominal degradation modes of the Alloy 22: general corrosion, microbially influenced corrosion, stress corrosion cracking, early failure due to manufacturing defects, and localized corrosion (LC). This paper specifically examines the incorporation of the Alloy 22 LC model into the Yucca Mountain TSPA model, particularly the abstraction and modeling methodology, as well as issues dealing with scaling, spatial variability, uncertainty, and coupling to other submodels that are part of the total system model, such as the submodel for seepage water chemistry.

Erbium is used as a storage medium for tritium. Microstructural study of helium bubble generation from tritium decay in erbium tritide can provide an unusual example of bubble development with negligible radiation damage. Aged erbium tritide film specimens were found to contain five distinctly different microstructural features. The general structure was of large columnar grains of ErT2. But on a fine scale, precipitates believed to be erbium oxy-tritides and helium bubbles could be identified. The precipitate size was in the range of ∼10 nm and the bubbles were of an unusual planar shape on {111} planes with an invariant thickness of ∼1 nm and a diameter on the order of 10 nm. Also, an outer layer containing no fine precipitate structure and only a few helium bubbles were present on the films. This layer is best described as a denuded zone which probably grew during aging in air. Finally, large embedded Er2O3 particles were found at low density and nonuniformly distributed, but sometimes extending through the thickness of the film. A failure mechanism allowing the helium to escape is suggested by observed cracking between bubbles closer to end of life. Copyright © 2007 by ASTM International.

Future energy systems based on gasification of coal or biomass for co-production of electrical power and fuels may require gas turbine operation on unusual gaseous fuel mixtures. In addition, global climate change concerns may dictate the generation of a CO2 product stream for end-use or sequestration, with potential impacts on the oxidizer used in the gas turbine. In this study the operation at atmospheric pressure of a small, optically accessible swirl-stabilized premixed combustor, burning fuels ranging from pure methane to conventional and H2-rich and H2-lean syngas mixtures is investigated. Both air and CO2-diluted oxygen are used as oxidizers. CO and NOx emissions for these flames have been determined from the lean blowout limit to slightly rich conditions (1.03). In practice, CO2-diluted oxygen systems will likely be operated close to stoichiometric conditions to minimize oxygen consumption while achieving acceptable NOx performance. The presence of hydrogen in the syngas fuel mixtures results in more compact, higher temperature flames, resulting in increased flame stability and higher NOx emissions. Consistent with previous experience, the stoichiometry of lean blowout decreases with increasing H2 content in the syngas. Similarly, the lean stoichiometry at which CO emissions become significant decreases with increasing H2 content. For the mixtures investigated, CO emissions near the stoichiometric point do not become significant until 0.95. At this stoichiometric limit, CO emissions rise more rapidly for combustion in O2-CO2 mixtures than for combustion in air.

Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many problems of interest. Informatics approaches attack the problem with empirical analysis of descriptions of chemical structure. The issue in these methods is how to describe molecules in a manner that facilitates accurate and general calculation of molecular properties. Here, we present a novel approach that utilizes aspects of simulation and informatics in order to formulate structure-property relationships. We show how supervised learning can be utilized to overcome the sampling problem in simulation approaches. Likewise, we show how learning can be achieved based on molecular descriptions that are rooted in the physics of dynamic intermolecular forces. We apply the approach to three problems including the analysis of corticosteroid binding globulin ligand binding affinity, identification of formylpeptide receptor ligands, and identification of resveratrol analogues capable of inhibiting activation of transcription factor nuclear factor kappaB. © 2008 American Chemical Society.

Abstract not provided.

In part I of this study we introduced a 17-parameter model that can predict heart rate regulation during postural change from sitting to standing. In this subsequent study, we focus on the 17 model parameters needed to adequately represent the observed heart rate response. In part I and in previous work (Olufsen et al. 2006), we estimated the 17 model parameters by minimizing the least squares error between computed and measured values of the heart rate using the Nelder-Mead method (a simplex algorithm). In this study, we compare the Nelder-Mead optimization method to two sampling methods: the implicit filtering method and a genetic algorithm. We show that these off-the-shelf optimization methods can work in conjunction with the heart rate model and provide reasonable parameter estimates with little algorithm tuning. In addition, we make use of the thousands of points sampled by the optimizers in the course of the minimization to perform an overall analysis of the model itself. Our findings show that the resulting least-squares problem has multiple local minima and that the non-linear-least squares error can vary over two orders of magnitude due to the complex interaction between the model parameters, even when provided with reasonable bound constraints. © Springer Science+Business Media, LLC 2007.

A method to measure interfacial mechanical properties at high temperatures and in a controlled atmosphere has been developed to study anodized aluminum surface coatings at temperatures where the interior aluminum alloy is molten. This is the first time that the coating strength has been studied under these conditions. We have investigated the effects of ambient atmosphere, temperature, and surface finish on coating strength for samples of aluminum alloy 7075. Surprisingly, the effective Young's modulus or strength of the coating when tested in air was twice as high as when samples were tested in an inert nitrogen or argon atmosphere. Additionally, the effective Young's modulus of the anodized coating increased with temperature in an air atmosphere but was independent of temperature in an inert atmosphere. The effect of surface finish was also examined. Sandblasting the surface prior to anodization was found to increase the strength of the anodized coating with the greatest enhancement noted for a nitrogen atmosphere. Machining marks were not found to significantly affect the strength.

Current published models for predicting squeeze film damping (SFD), which are based on different assumptions, give widely different results in the free-molecule regime. The work presented here provides experimental data for validating SFD models in that regime. The test device was an almost rectangular micro plate supported by beam springs. The structure was base-excited. The rigid plate oscillated vertically while staying parallel to the substrate. The velocities of the plate and of the substrate were measured with a laser Doppler vibrometer and a microscope. The damping ratio was calculated by performing modal analysis of the frequency response functions. The test structures were contained in a vacuum chamber with air pressures controlled to provide a five-order-of-magnitude range of Knudsen numbers. The damping coefficients from the measurements were compared with predictions from various published models. The results show that the continuum-base Reynolds equation predicts squeeze-film damping accurately if used with correct boundary conditions. The accuracy of molecular-based models depends heavily on the assumptions used in developing the models. Copyright © 2007 by ASME.