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Final Progress Report

Description: The BIOMOL grant was for 'Local System Support for PDB Biological Unit Search and Display' to augment Rasmol's [Bernstein 2000] [Sayle, Milner-White 1995] existing macromolecular display functions with new capabilities by taking advantage of recent increases in local computing power in order to move functionality that is now scattered among various local and remote systems into one local package. Work included new algorithms for molecular surface display, an extended format for Protein Data Bank Entries, work on issues relating to the integration of multiple diffraction images formats.
Date: February 6, 2012
Creator: Bernstein, Herbert J.

Final report

Description: High performance computational science and engineering simulations have become an increasingly important part of the scientist's problem solving toolset. A key reason is the development of widely used codes and libraries that support these applications, for example, Netlib, a collection of numerical libraries [33]. The term community codes refers to those libraries or applications that have achieved some critical level of acceptance by a user community. Many of these applications are on the high-end in terms of required resources: computation, storage, and communication. Recently, there has been considerable interest in putting such applications on-line and packaging them as network services to make them available to a wider user base. Applications such as data mining [22], theorem proving and logic [14], parallel numerical computation [8][32] are example services that are all going on-line. Transforming applications into services has been made possible by advances in packaging and interface technologies including component systems [2][6][13][28][37], proposed communication standards [34], and newer Web technologies such as Web Services [38]. Network services allow the user to focus on their application and obtain remote service when needed by simply invoking the service across the network. The user can be assured that the most recent version of the code or service is always provided and they do not need to install, maintain, and manage significant infrastructure to access the service. For high performance applications in particular, the user is still often required to install a code base (e.g. MPI), and therefore become involved with the tedious details of infrastructure management. In the network service model, the service provider is responsible for all of these activities and not the user. The user need not become an expert in high performance computing. An additional advantage of high-end network services is that the user need not have specialized computational resources in ...
Date: April 30, 2006
Creator: Weissman, Jon B

Community Assessment Tool for Public Health Emergencies Including Pandemic Influenza

Description: The Community Assessment Tool (CAT) for Public Health Emergencies Including Pandemic Influenza (hereafter referred to as the CAT) was developed as a result of feedback received from several communities. These communities participated in workshops focused on influenza pandemic planning and response. The 2008 through 2011 workshops were sponsored by the Centers for Disease Control and Prevention (CDC). Feedback during those workshops indicated the need for a tool that a community can use to assess its readiness for a disaster—readiness from a total healthcare perspective, not just hospitals, but the whole healthcare system. The CAT intends to do just that—help strengthen existing preparedness plans by allowing the healthcare system and other agencies to work together during an influenza pandemic. It helps reveal each core agency partners' (sectors) capabilities and resources, and highlights cases of the same vendors being used for resource supplies (e.g., personal protective equipment [PPE] and oxygen) by the partners (e.g., public health departments, clinics, or hospitals). The CAT also addresses gaps in the community's capabilities or potential shortages in resources. While the purpose of the CAT is to further prepare the community for an influenza pandemic, its framework is an extension of the traditional all-hazards approach to planning and preparedness. As such, the information gathered by the tool is useful in preparation for most widespread public health emergencies. This tool is primarily intended for use by those involved in healthcare emergency preparedness (e.g., community planners, community disaster preparedness coordinators, 9-1-1 directors, hospital emergency preparedness coordinators). It is divided into sections based on the core agency partners, which may be involved in the community's influenza pandemic influenza response.
Date: April 14, 2011
Creator: HCTT-CHE

Data Quality Assessment and Control for the ARM Climate Research Facility

Description: The mission of the Atmospheric Radiation Measurement (ARM) Climate Research Facility is to provide observations of the earth climate system to the climate research community for the purpose of improving the understanding and representation, in climate and earth system models, of clouds and aerosols as well as their coupling with the Earth's surface. In order for ARM measurements to be useful toward this goal, it is important that the measurements are of a known and reasonable quality. The ARM data quality program includes several components designed to identify quality issues in near-real-time, track problems to solutions, assess more subtle long-term issues, and communicate problems to the user community.
Date: June 26, 2012
Creator: Peppler, R.

Quarterly VAP Report - April to June

Description: The purpose of this report is to provide a concise status update for value-added products (VAP) implemented by the Atmospheric Radiation Measurement Climate Research Facility. The report is divided into the following sections: (1) new VAPs for which development has begun, (2) progress on existing VAPs, (3) future VAPs that have been recently approved, (4) other work that leads to a VAP, and (5) top requested VAPs from the Data Archive. New information is highlighted in blue text. New information about processed data by the developer is highlighted in red text. The upcoming milestones and dates are highlighted in green.
Date: August 20, 2012
Creator: Sivaraman, C

Quarterly VAP Report - January to March

Description: The purpose of this report is to provide a concise status update for value-added products (VAP) implemented by the Atmospheric Radiation Measurement Climate Research Facility. The report is divided into the following sections: (1) new VAPs for which development has begun, (2) progress on existing VAPs, (3) future VAPs that have been recently approved, (4) other work that leads to a VAP, and (5) top requested VAPs from the archive. New information is highlighted in blue text. New information about processed data by the developer is highlighted in red text. The upcoming milestones and dates are highlighted in green.
Date: June 7, 2012
Creator: Sivaraman, C

CRADA Final Report, 2011S003, Faraday Technologies

Description: This Phase I SBIR program addressed the need for an improved manufacturing process for electropolishing niobium RF superconducting cavities for the International Linear Collider (ILC). The ILC is a proposed particle accelerator that will be used to gain a deeper understanding of the forces of energy and matter by colliding beams of electrons and positrons at nearly the speed of light. The energy required for this to happen will be achieved through the use of advanced superconducting technology, specifically ~16,000 RF superconducting cavities operating at near absolute zero. The RF superconductor cavities will be fabricated from highly pure Nb, which has an extremely low surface resistance at 2 Kelvin when compared to other materials. To take full advantage of the superconducting properties of the Nb cavities, the inner surface must be a) polished to a microscale roughness < 0.1 µm with removal of at least 100 µm of material, and b) cleaned to be free of impurities that would degrade performance of the ILC. State-of-the-art polishing uses either chemical polishing or electropolishing, both of which require hydrofluoric acid to achieve breakdown of the strong passive film on the surface. In this Phase I program, Faraday worked with its collaborators at the Thomas Jefferson National Accelerator Facility (JLab) to demonstrate the feasibility of an electropolishing process for pure niobium, utilizing an environmentally benign alternative to chemical or electrochemical polishing electrolytes containing hydrofluoric acid. Faraday utilized a 31 wt% aqueous sulfuric acid solution (devoid of hydrofluoric acid) in conjunction with the FARADAYICSM Process, which uses pulse/pulse reverse fields for electropolishing, to demonstrate the ability to electropolish niobium to the desired surface finish. The anticipated benefits of the FARADAYICSM Electropolishing process will be a simpler, safer, and less expensive method capable of surface finishing high purity niobium cavities. Another potential benefit would be ...
Date: December 12, 2012
Creator: Technologies, Faraday

MOGO: Model-Oriented Global Optimization of Petascale Applications

Description: The MOGO project was initiated under in 2008 under the DOE Program Announcement for Software Development Tools for Improved Ease-of-Use on Petascale systems (LAB 08-19). The MOGO team consisted of Oak Ridge National Lab, Argonne National Lab, and the University of Oregon. The overall goal of MOGO was to attack petascale performance analysis by developing a general framework where empirical performance data could be efficiently and accurately compared with performance expectations at various levels of abstraction. This information could then be used to automatically identify and remediate performance problems. MOGO was be based on performance models derived from application knowledge, performance experiments, and symbolic analysis. MOGO was able to make reasonable impact on existing DOE applications and systems. New tools and techniques were developed, which, in turn, were used on important DOE applications on DOE LCF systems to show significant performance improvements.
Date: September 14, 2012
Creator: Malony, Allen D. & Shende, Sameer S.

Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials

Description: This report contains a summary of progress made on the subtask area on phase field model development for microstructure evolution in irradiated materials, which was a part of the Computational Materials Science Network (CMSN) project entitled: Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials. The model problem chosen has been that of void nucleation and growth under irradiation conditions in single component systems.
Date: May 28, 2012
Creator: El-Azab, Anter

Physics Opportunities with the 12 GeV Upgrade at Jefferson Lab

Description: We are at the dawn of a new era in the study of hadronic nuclear physics. The non-Abelian nature of Quantum Chromodynamics (QCD) and the resulting strong coupling at low energies represent a significant challenge to nuclear and particle physicists. The last decade has seen the development of new theoretical and experimental tools to quantitatively study the nature of confinement and the structure of hadrons comprised of light quarks and gluons. Together these will allow both the spectrum and the structure of hadrons to be elucidated in unprecedented detail. Exotic mesons that result from excitation of the gluon field will be explored. Multidimensional images of hadrons with great promise to reveal the dynamics of the key underlying degrees of freedom will be produced. In particular, these multidimensional distributions open a new window on the elusive spin content of the nucleon through observables that are directly related to the orbital angular momenta of quarks and gluons. Moreover, computational techniques in Lattice QCD now promise to provide insightful and quantitative predictions that can be meaningfully confronted with, and elucidated by, forthcoming experimental data. In addition, the development of extremely high intensity, highly polarized and extraordinarily stable beams of electrons provides innovative opportunities for probing (and extending) the Standard Model, both through parity violation studies and searches for new particles. Thus the 12 GeV upgrade of the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab will enable a new experimental program with substantial discovery potential to address these and other important topics in nuclear, hadronic and electroweak physics.
Date: August 1, 2012
Creator: Dudek, Jozef; Essig, Rouven; Kumar, Krishna; Meyer, Curtis; McKeown, Robert; Meziani, Zein Eddine et al.

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

Description: Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when applied to the manually curated training set. Applying this method to the data representing around a quarter of the fraction space for water soluble proteins in D. vulgaris, we obtained 854 reliable ...
Date: May 26, 2011
Creator: Baliga, Nitin S.

Journal of Undergraduate Research, Volume I, 2001

Description: This is our first volume of the Undergraduate Journal. It is an approbation of the impressive research performed by summer interns under the guidance of their dedicated mentors. The full-length publications were chosen from a pool of submissions that were reviewed by many of the excellent scientists at our National Laboratories. Most of these students will pursue careers in science, engineering and technology and, hopefully, some of this talent will remain with our labs. We have also included about 125 abstracts that survived the review process. These were submitted from all of our participating National Laboratories.
Date: January 1, 2001
Creator: Faletra, P.; Beavis, W.; Franz, K.; Musick, C.; Walbridge, S.E. & Myron, H.

Charter for the ARM Climate Research Facility Science Board

Description: The objective of the ARM Science Board is to promote the Nation’s scientific enterprise by ensuring that the best quality science is conducted at the DOE’s User Facility known as the ARM Climate Research Facility. The goal of the User Facility is to serve scientific researchers by providing unique data and tools to facilitate scientific applications for improving understanding and prediction of climate science.
Date: March 8, 2013
Creator: Ferrell, W

ARM Climate Research Facility Quarterly Value-Added Product Report First Quarter: October 01-December 31, 2011

Description: The purpose of this report is to provide a concise status update for value-added products (VAP) implemented by the Atmospheric Radiation Measurement (ARM) Climate Research Facility. The report is divided into the following sections: (1) new VAPs for which development has begun, (2) progress on existing VAPs, (3) future VAPs that have been recently approved, (4) other work that leads to a VAP, and (5) top requested VAPs from the archive.
Date: February 28, 2012
Creator: Sivaraman, C

ARM Climate Research Facility Quarterly Value-Added Product Report Fourth Quarter: July 1–September 30, 2012

Description: The purpose of this report is to provide a concise status update for value-added products (VAP) implemented by the Atmospheric Radiation Measurement (ARM) Climate Research Facility. The report is divided into the following sections: (1) new VAPs for which development has begun, (2) progress on existing VAPs, (3) future VAPs that have been recently approved, (4) other work that leads to a VAP, and (5) top requested VAPs from the archive.
Date: November 13, 2012
Creator: Sivaraman, C.