Classifying proteins by common conserved motifs to control ligand binding specificity.
Abstract not provided.
Anderson, Peter↗
Engineering topics
De Sapio, Vincent
Publications and source records attributed to De Sapio, Vincent.
A Task-level Biomechanical Framework for Investigating Motion Control in Humans.
Abstract not provided.
De Sapio, Vincent↗
Biotechnology development for biomedical applications.
Sandia's scientific and engineering expertise in the fields of computational biology, high-performance prosthetic limbs, biodetection, and bioinformatics has been applied to specific problems at the forefront of cancer research. Molecular modeling was employed to design stable mutations of the enzyme L-asparaginase with improved selectivity for asparagine over other amino acids with the potential for improved cancer chemotherapy. New electrospun polymer composites with improved electrical conductivity and mechanical compliance have been demonstrated with the promise of direct interfacing between the peripheral nervous system and the control electronics of advanced prosthetics. The capture of rare circulating tumor cells has been demonstrated on a microfluidic chip produced with a versatile fabrication processes capable of integration with existing lab-on-a-chip and biosensor technology. And software tools have been developed to increase the calculation speed of clustered heat maps for the display of relationships in large arrays of protein data. All these projects were carried out in collaboration with researchers at the University of Texas M. D. Anderson Cancer Center in Houston, TX.
59 BASIC BIOLOGICAL SCIENCES↗
Long-term Archival and Retrieval of Engineering Data: Implications for the DART Workbench
Long term archival and retrieval of engineering data is a key component of product life cycle management. Standards have emerged over time to facilitate archival and retrieval, particularly with respect to CAD data. In this report we assess the state of the art in industry, academia, and government, with respect to archival management and preservation planning. Additionally, we present different scenarios for the integration of the DART Workbench tool with an archival and retrieval system. These scenarios are based on existing CAD/CAE industry standards as well as Semantic Web technologies. The goal is not to design and implement a long-term archival system, but rather, to anticipate potential future systems and consider how the DART Workbench may integrate with them. A secondary goal is to provide some reasoned input for eventual lab-wide implementation of a particular approach, thus steering the design of such a system to some degree.
De Sapio, Vincent↗
Tuning molecular specificity for design of medical countermeasures.
Abstract not provided.
Roe, Diana C.↗
Scalable HPC monitoring and analysis for understanding and automated response.
No abstract prepared.
99 GENERAL AND MISCELLANEOUS↗
The application of quaternions and other spatial representations to the reconstruction of re-entry vehicle motion.
The analysis of spacecraft kinematics and dynamics requires an efficient scheme for spatial representation. While the representation of displacement in three dimensional Euclidean space is straightforward, orientation in three dimensions poses particular challenges. The unit quaternion provides an approach that mitigates many of the problems intrinsic in other representation approaches, including the ill-conditioning that arises from computing many successive rotations. This report focuses on the computational utility of unit quaternions and their application to the reconstruction of re-entry vehicle (RV) motion history from sensor data. To this end they will be used in conjunction with other kinematic and data processing techniques. We will present a numerical implementation for the reconstruction of RV motion solely from gyroscope and accelerometer data. This will make use of unit quaternions due to their numerical efficacy in dealing with the composition of many incremental rotations over a time series. In addition to signal processing and data conditioning procedures, algorithms for numerical quaternion-based integration of gyroscope data will be addressed, as well as accelerometer triangulation and integration to yield RV trajectory. Actual processed flight data will be presented to demonstrate the implementation of these methods.
47 OTHER INSTRUMENTATION↗
Understanding large scale HPC systems through scalable monitoring and analysis.
As HPC systems grow in size and complexity, diagnosing problems and understanding system behavior, including failure modes, becomes increasingly difficult and time consuming. At Sandia National Laboratories we have developed a tool, OVIS, to facilitate large scale HPC system understanding. OVIS incorporates an intuitive graphical user interface, an extensive and extendable data analysis suite, and a 3-D visualization engine that allows visual inspection of both raw and derived data on a geometrically correct representation of a HPC system. This talk will cover system instrumentation, data collection (including log files and the complications of meaningful parsing), analysis, visualization of both raw and derived information, and how data can be combined to increase system understanding and efficiency.
99 GENERAL AND MISCELLANEOUS↗
A framework for graph-based synthesis, analysis, and visualization of HPC cluster job data.
The monitoring and system analysis of high performance computing (HPC) clusters is of increasing importance to the HPC community. Analysis of HPC job data can be used to characterize system usage and diagnose and examine failure modes and their effects. This analysis is not straightforward, however, due to the complex relationships that exist between jobs. These relationships are based on a number of factors, including shared compute nodes between jobs, proximity of jobs in time, etc. Graph-based techniques represent an approach that is particularly well suited to this problem, and provide an effective technique for discovering important relationships in job queuing and execution data. The efficacy of these techniques is rooted in the use of a semantic graph as a knowledge representation tool. In a semantic graph job data, represented in a combination of numerical and textual forms, can be flexibly processed into edges, with corresponding weights, expressing relationships between jobs, nodes, users, and other relevant entities. This graph-based representation permits formal manipulation by a number of analysis algorithms. This report presents a methodology and software implementation that leverages semantic graph-based techniques for the system-level monitoring and analysis of HPC clusters based on job queuing and execution data. Ontology development and graph synthesis is discussed with respect to the domain of HPC job data. The framework developed automates the synthesis of graphs from a database of job information. It also provides a front end, enabling visualization of the synthesized graphs. Additionally, an analysis engine is incorporated that provides performance analysis, graph-based clustering, and failure prediction capabilities for HPC systems.
97 MATHEMATICS AND COMPUTING↗