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open access

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

Description: Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more s… more
Date: November 29, 2010
Creator: Zemla, A; Lang, D; Kostova, T; Andino, R & Zhou, C
Partner: UNT Libraries Government Documents Department
open access

Sensor Configuration Selection for Discrete-Event Systems under Unreliable Observations

Description: Algorithms for counting the occurrences of special events in the framework of partially-observed discrete event dynamical systems (DEDS) were developed in previous work. Their performances typically become better as the sensors providing the observations become more costly or increase in number. This paper addresses the problem of finding a sensor configuration that achieves an optimal balance between cost and the performance of the special event counting algorithm, while satisfying given obser… more
Date: August 1, 2010
Creator: Lin, Wen-Chiao; Yoo, Tae-Sic & Garcia, Humberto E.
Partner: UNT Libraries Government Documents Department
open access

U.S. Department of Energy Best Practices Workshop onFile Systems & Archives San Francisco, CA September 26-27, 2011 Position Paper

Description: This position paper discusses issues of usability of the large parallel file systems in the Livermore Computing Center. The primary uses of these file systems are for storage and access of data that is created during the course of a simulation running on an LC system. The Livermore Computing Center has multiple, globally mounted parallel file systems in each of its computing environments. The single biggest issue of file system usability that we have encountered through the years is to maintain… more
Date: September 1, 2011
Creator: Hedges, R M
Partner: UNT Libraries Government Documents Department
open access

P50/P90 Analysis for Solar Energy Systems Using the System Advisor Model: Preprint

Description: To secure competitive financing for a solar energy generation project, the economic risk associated with interannual solar resource variability must be quantified. One way to quantify this risk is to calculate exceedance probabilities representing the amount of energy expected to be produced by a plant. Many years of solar radiation and metereological data are required to determine these values, often called P50 or P90 values for the level of certainty they represent. This paper describes the t… more
Date: June 1, 2012
Creator: Dobos, A. P.; Gilman, P. & Kasberg, M.
Partner: UNT Libraries Government Documents Department
open access

Case Studies Comparing System Advisor Model (SAM) Results to Real Performance Data: Preprint

Description: NREL has completed a series of detailed case studies comparing the simulations of the System Advisor Model (SAM) and measured performance data or published performance expectations. These case studies compare PV measured performance data with simulated performance data using appropriate weather data. The measured data sets were primarily taken from NREL onsite PV systems and weather monitoring stations.
Date: June 1, 2012
Creator: Blair, N.; Dobos, A. & Sather, N.
Partner: UNT Libraries Government Documents Department
open access

Effect of Coal Properties and Operation Conditions on Flow Behavior of Coal Slag in Entrained Flow Gasifiers: A Brief Review

Description: Integrated gasification combined cycle (IGCC) is a potentially promising clean technology with an inherent advantage of low emissions, since the process removes contaminants before combustion instead of from flue gas after combustion, as in a conventional coal steam plant. In addition, IGCC has potential for cost-effective carbon dioxide capture. Availability and high capital costs are the main challenges to making IGCC technology more competitive and fully commercial. Experiences from demonstr… more
Date: January 1, 2011
Creator: Wang,Ping & Massoudi, Mehrdad
Partner: UNT Libraries Government Documents Department
open access

The Network Completion Problem: Inferring Missing Nodes and Edges in Networks

Description: Network structures, such as social networks, web graphs and networks from systems biology, play important roles in many areas of science and our everyday lives. In order to study the networks one needs to first collect reliable large scale network data. While the social and information networks have become ubiquitous, the challenge of collecting complete network data still persists. Many times the collected network data is incomplete with nodes and edges missing. Commonly, only a part of the ne… more
Date: November 14, 2011
Creator: Kim, M & Leskovec, J
Partner: UNT Libraries Government Documents Department
open access

Performance Portability for Unstructured Mesh Physics

Description: ASC legacy software must be ported to emerging hardware architectures. This paper notes that many programming models used by DOE applications are similar, and suggests that constructing a common terminology across these models could reveal a performance portable programming model. The paper then highlights how the LULESH mini-app is used to explore new programming models with outside solution providers. Finally, we suggest better tools to identify parallelism in software, and give suggestions f… more
Date: March 23, 2012
Creator: Keasler, J A
Partner: UNT Libraries Government Documents Department
open access

Review of Prior U.S. Attribute Measurement Systems

Description: Attribute Measurement Systems have been developed and demonstrated several times in the United States over the last decade or so; under the Trilateral Initiative (1996-2002), FMTTD (Fissile Material Transparency Technology Demonstration, 2000), and NG-AMS (Next Generation Attribute Measurement System, 2005-2008). Each Attribute Measurement System has contributed to the growing body of knowledge regarding the use of such systems in warhead dismantlement and other Arms Control scenarios. The Tril… more
Date: July 6, 2012
Creator: White, G K
Partner: UNT Libraries Government Documents Department
open access

Modeling Personalized Email Prioritization: Classification-based and Regression-based Approaches

Description: Email overload, even after spam filtering, presents a serious productivity challenge for busy professionals and executives. One solution is automated prioritization of incoming emails to ensure the most important are read and processed quickly, while others are processed later as/if time permits in declining priority levels. This paper presents a study of machine learning approaches to email prioritization into discrete levels, comparing ordinal regression versus classier cascades. Given the or… more
Date: October 24, 2011
Creator: Yoo, S.; Yang, Y. & Carbonell, J.
Partner: UNT Libraries Government Documents Department
open access

A Freestream-Preserving High-Order Finite-Volume Method for Mapped Grids with Adaptive-Mesh Refinement

Description: A fourth-order accurate finite-volume method is presented for solving time-dependent hyperbolic systems of conservation laws on mapped grids that are adaptively refined in space and time. Novel considerations for formulating the semi-discrete system of equations in computational space combined with detailed mechanisms for accommodating the adapting grids ensure that conservation is maintained and that the divergence of a constant vector field is always zero (freestream-preservation property). A… more
Date: December 16, 2011
Creator: Guzik, S.; McCorquodale, P. & Colella, P.
Partner: UNT Libraries Government Documents Department
open access

Selecting Observation Platforms for Optimized Anomaly Detectability under Unreliable Partial Observations

Description: Diagnosers for keeping track on the occurrences of special events in the framework of unreliable partially observed discrete-event dynamical systems were developed in previous work. This paper considers observation platforms consisting of sensors that provide partial and unreliable observations and of diagnosers that analyze them. Diagnosers in observation platforms typically perform better as sensors providing the observations become more costly or increase in number. This paper proposes a met… more
Date: June 1, 2011
Creator: Lin, Wen-Chiao; Garcia, Humberto E. & Yoo, Tae-Sic
Partner: UNT Libraries Government Documents Department
open access

Value of Geographic Diversity of Wind and Solar: Stochastic Geometry Approach; Preprint

Description: Based on the available geographically dispersed data for the continental U.S. (excluding Alaska), we analyze to what extent the geographic diversity of these resources can offset their variability. A geometric model provides a convenient measure for resource variability, shows the synergy between wind and solar resources.
Date: August 1, 2012
Creator: Diakov, V.
Partner: UNT Libraries Government Documents Department
open access

Understanding Performance of Parallel Scientific Simulation Codes using Open|SpeedShop

Description: Conclusions of this presentation are: (1) Open SpeedShop's (OSS) is convenient to use for large, parallel, scientific simulation codes; (2) Large codes benefit from uninstrumented execution; (3) Many experiments can be run in a short time - might need multiple shots e.g. usertime for caller-callee, hwcsamp for HW counters; (4) Decent idea of code's performance is easily obtained; (5) Statistical sampling calls for decent number of samples; and (6) HWC data is very useful for micro-analysis but … more
Date: November 7, 2011
Creator: Ghosh, K K
Partner: UNT Libraries Government Documents Department
open access

Rapid Application Development with OpenStudio: Preprint

Description: This paper presents several case studies of rapidly implemented, audience-specific applications for whole building energy modeling and standards analysis. By tailoring each application to the audience and the task at hand, the required learning curve for new users was greatly reduced. Each case study used OpenStudio, the U.S. Department of Energy's middleware software development kit (SDK). OpenStudio provides an easy interface to the EnergyPlus whole building simulation engine, while extending… more
Date: May 1, 2012
Creator: Weaver, E.; Long, N.; Fleming, K.; Schott, M.; Benne, K. & Hale, E.
Partner: UNT Libraries Government Documents Department
open access

Benchmarking of Graphite Reflected Critical Assemblies of UO2

Description: A series of experiments were carried out in 1963 at the Oak Ridge National Laboratory Critical Experiments Facility (ORCEF) for use in space reactor research programs. A core containing 93.2% enriched UO2 fuel rods was used in these experiments. The first part of the experimental series consisted of 253 tightly-packed fuel rods (1.27 cm triangular pitch) with graphite reflectors [1], the second part used 253 graphite-reflected fuel rods organized in a 1.506 cm triangular pitch [2], and the fina… more
Date: November 1, 2011
Creator: Marshall, Margaret A. & Bess, John D.
Partner: UNT Libraries Government Documents Department
open access

Fault Tolerance and Scaling in e-Science Cloud Applications: Observations from the Continuing Development of MODISAzure

Description: It can be natural to believe that many of the traditional issues of scale have been eliminated or at least greatly reduced via cloud computing. That is, if one can create a seemingly wellfunctioning cloud application that operates correctly on small or moderate-sized problems, then the very nature of cloud programming abstractions means that the same application will run as well on potentially significantly larger problems. In this paper, we present our experiences taking MODISAzure, our satell… more
Date: April 1, 2010
Creator: Li, Jie; Humphrey, Marty; Cheah, You-Wei; Ryu, Youngryel; Agarwal, Deb; Jackson, Keith et al.
Partner: UNT Libraries Government Documents Department
open access

Extended Forward Sensitivity Analysis for Uncertainty Quantification

Description: Verification and validation (V&V) are playing more important roles to quantify uncertainties and realize high fidelity simulations in engineering system analyses, such as transients happened in a complex nuclear reactor system. Traditional V&V in the reactor system analysis focused more on the validation part or did not differentiate verification and validation. The traditional approach to uncertainty quantification is based on a 'black box' approach. The simulation tool is treated as a… more
Date: September 1, 2011
Creator: Zhao, Haihua & Mousseau, Vincent A.
Partner: UNT Libraries Government Documents Department
open access

Towards Resilient Critical Infrastructures: Application of Type-2 Fuzzy Logic in Embedded Network Security Cyber Sensor

Description: Resiliency and cyber security of modern critical infrastructures is becoming increasingly important with the growing number of threats in the cyber-environment. This paper proposes an extension to a previously developed fuzzy logic based anomaly detection network security cyber sensor via incorporating Type-2 Fuzzy Logic (T2 FL). In general, fuzzy logic provides a framework for system modeling in linguistic form capable of coping with imprecise and vague meanings of words. T2 FL is an extension… more
Date: August 1, 2011
Creator: Linda, Ondrej; Vollmer, Todd; Alves-Foss, Jim & Manic, Milos
Partner: UNT Libraries Government Documents Department
open access

Tuning HDF5 for Lustre File Systems

Description: HDF5 is a cross-platform parallel I/O library that is used by a wide variety of HPC applications for the flexibility of its hierarchical object-database representation of scientific data. We describe our recent work to optimize the performance of the HDF5 and MPI-IO libraries for the Lustre parallel file system. We selected three different HPC applications to represent the diverse range of I/O requirements, and measured their performance on three different systems to demonstrate the robustness … more
Date: September 24, 2010
Creator: Howison, Mark; Koziol, Quincey; Knaak, David; Mainzer, John & Shalf, John
Partner: UNT Libraries Government Documents Department
open access

Feature-Based Statistical Analysis of Combustion Simulation Data

Description: We present a new framework for feature-based statistical analysis of large-scale scientific data and demonstrate its effectiveness by analyzing features from Direct Numerical Simulations (DNS) of turbulent combustion. Turbulent flows are ubiquitous and account for transport and mixing processes in combustion, astrophysics, fusion, and climate modeling among other disciplines. They are also characterized by coherent structure or organized motion, i.e. nonlocal entities whose geometrical features… more
Date: November 18, 2011
Creator: Bennett, J; Krishnamoorthy, V; Liu, S; Grout, R; Hawkes, E; Chen, J et al.
Partner: UNT Libraries Government Documents Department
open access

Selective Electrocatalytic Activity of Ligand Stabilized Copper Oxide Nanoparticles

Description: Ligand stabilization can influence the surface chemistry of Cu oxide nanoparticles (NPs) and provide unique product distributions for electrocatalytic methanol (MeOH) oxidation and CO{sub 2} reduction reactions. Oleic acid (OA) stabilized Cu{sub 2}O and CuO NPs promote the MeOH oxidation reaction with 88% and 99.97% selective HCOH formation, respectively. Alternatively, CO{sub 2} is the only reaction product detected for bulk Cu oxides and Cu oxide NPs with no ligands or weakly interacting liga… more
Date: January 1, 2011
Creator: Kauffman, Douglas R.; Ohodnicki, Paul R.; Kail, Brian W & Matranga, Christopher
Partner: UNT Libraries Government Documents Department
open access

Developing extensible lattice-Boltzmann simulators for general-purpose graphics-processing units

Description: Lattice-Boltzmann methods are versatile numerical modeling techniques capable of reproducing a wide variety of fluid-mechanical behavior. These methods are well suited to parallel implementation, particularly on the single-instruction multiple data (SIMD) parallel processing environments found in computer graphics processing units (GPUs). Although more recent programming tools dramatically improve the ease with which GPU programs can be written, the programming environment still lacks the flexi… more
Date: December 21, 2011
Creator: Walsh, S C & Saar, M O
Partner: UNT Libraries Government Documents Department
open access

Direct-Steam Linear Fresnel Performance Model for NREL's System Advisor Model

Description: This paper presents the technical formulation and demonstrated model performance results of a new direct-steam-generation (DSG) model in NREL's System Advisor Model (SAM). The model predicts the annual electricity production of a wide range of system configurations within the DSG Linear Fresnel technology by modeling hourly performance of the plant in detail. The quasi-steady-state formulation allows users to investigate energy and mass flows, operating temperatures, and pressure drops for geom… more
Date: September 1, 2012
Creator: Wagner, M. J. & Zhu, G.
Partner: UNT Libraries Government Documents Department
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