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We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

The majority of US commercial floor space is cooled by rooftop HVAC units (RTU's). RTU popularity derives chiefly from their low initial cost and relative ease of service access without disturbing building occupants. Unfortunately, current RTU's are inherently inefficient due to a combination of characteristics that unnecessarily increase cooling loads and energy use. Existing RTU's in the U.S. consume an estimated 2.4 quads annually. Inefficient RTU's create an estimated 3.5% of U.S. CO{sub 2} emissions, thus contributing significantly to global warming. Also, RTU's often fail to maintain adequate ventilation air and air filtration. This project was developed to evaluate the feasibility of a radically new ''HyPak'' RTU design that significantly and cost-effectively increases RTU performance and delivered air quality. The objective of the HyPak Project was to design, develop and test a hydronic RTU that provides a quantum improvement over conventional RTU performance. Our proposal targeted 60% and 50% reduction in electrical energy use by the HyPak RTU for dry and humid climates, respectively, when compared with a conventional unit.

Testimony issued by the General Accounting Office with an abstract that begins "The National Defense Authorization Act for Fiscal Year 2002 authorized an additional Base Realignment and Closure (BRAC) round in 2005. The legislation requires the Department of Defense (DOD) to provide Congress in early 2004 with a report that addresses excess infrastructure and certifies that an additional BRAC round is needed and that annual net savings will be realized by each military department not later than fiscal year 2011. GAO is required to assess this information as well as the selection criteria for the 2005 round and report to Congress within 60 days of DOD's submission. The legislation also retains the requirement for GAO to assess the BRAC 2005 decisionmaking process and resulting recommendations. This testimony addresses (1) the BRAC process from a historical perspective, (2) GAO's role in the process, and (3) GAO's initial observations on key issues DOD is required to address in preparation for the 2005 round. Because DOD had not submitted its required 2004 report at the time we completed this statement, this testimony relies on our prior work that addressed issues associated with excess capacity and BRAC savings."

This report explores the intellectual property laws and policies concerning the parallel importation of patented pharmaceuticals into the United States.

In a new mode of measurement, the amplitude of a tearing mode rotating at frequencies of up to tens of KHz has been obtained using the spectral features of high frequency MSE data. A formulation has been developed to calculate the pitch angle oscillations associated with these instabilities, from the MSE spectrum. Density fluctuations can be simultaneously obtained from MSE measurements if the intensity response to density variation can be calibrated. Examples of observations are given and detection limits are explored.

Externally dispersed interferometry (EDI) is a technique for enhancing the performance of spectrographs for wide bandwidth high resolution spectroscopy and Doppler radial velocimetry. By placing a small angle-independent interferometer near the slit of a spectrograph, periodic fiducials are embedded on the recorded spectrum. The multiplication of the stellar spectrum times the sinusoidal fiducial net creates a moir{acute e} pattern, which manifests high detailed spectral information heterodyned down to detectably low spatial frequencies. The latter can more accurately survive the blurring, distortions and CCD Nyquist limitations of the spectrograph. Hence lower resolution spectrographs can be used to perform high resolution spectroscopy and radial velocimetry. Previous demonstrations of {approx}2.5x resolution boost used an interferometer having a single fixed delay. We report new data indicating {approx}6x Gaussian resolution boost (140,000 from a spectrograph with 25,000 native resolving power), taken by using multiple exposures at widely different interferometer delays.

In order to obtain formulas providing estimates for elastic constants of random polycrystals of laminates, some known rigorous bounds of Peselnick, Meister, and Watt are first simplified. Then, some new self-consistent estimates are formulated based on the resulting analytical structure of these bounds. A numerical study is made, assuming first that the internal structure (i.e., the laminated grain structure) is not known, and then that it is known. The purpose of this aspect of the study is to attempt to quantify the differences in the predictions of properties of the same system being modeled when such internal structure of the composite medium and spatial correlation information is and is not available.

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An adaptive optical system used to correct horizontal beam propagation paths has been demonstrated. This system utilizes an interferometric wave-front sensor and a large-actuator-number MEMS-based spatial light modulator to correct the aberrations incurred by the beam after propagation along the path. Horizontal path correction presents a severe challenge to adaptive optics systems due to the short atmospheric transverse coherence length and the high degree of scintillation incurred by laser propagation along these paths. Unlike wave-front sensors that detect phase gradients, however, the interferometric wave-front sensor measures the wrapped phase directly. Because the system operates with nearly monochromatic light and uses a segmented spatial light modulator, it does not require that the phase be unwrapped to provide a correction and it also does not require a global reconstruction of the wave-front to determine the phase as required by gradient detecting wave-front sensors. As a result, issues with branch points are eliminated. Because the atmospheric probe beam is mixed with a large amplitude reference beam, it can be made to operate in a photon noise limited regime making its performance relatively unaffected by scintillation. The MEMS-based spatial light modulator in the system contains 1024 pixels and is controlled to speeds in excess …

The Republic of Kazakhstan is continuing to develop its extensive petroleum reserves in the Tengiz region of the northeastern part of the Caspian Sea. Large quantities of by-product sulfur are being produced as a result of the removal of hydrogen sulfide from the oil and gas produced in the region. Lack of local markets and economic considerations limit the traditional outlets for by-product sulfur and the buildup of excess sulfur is a becoming a potential economic and environmental liability. Thus, new applications for re-use of by-product sulfur that will benefit regional economies including construction, paving and waste treatment are being developed. One promising application involves the cleanup and treatment of mercury at a Kazakhstan chemical plant. During 19 years of operation at the Pavlodar Khimprom chlor-alkali production facility, over 900 tons of mercury was lost to the soil surrounding and beneath the buildings. The Institute of Metallurgy and Ore Benefication (Almaty) is leading a team to develop and demonstrate a vacuum-assisted thermal process to extract the mercury from the soil and concentrate it as pure, elemental mercury, which will then be treated using the Sulfur Polymer Stabilization/Solidification (SPSS) process. The use of locally produced sulfur will recycle a low-value industrial …

We consider the collinear limit of QCD amplitudes at one-loop order, and their factorization properties directly in color space. These results apply to the multiple collinear limit of an arbitrary number of QCD partons, and are a basic ingredient in many higher-order computations. In particular, we discuss the triple collinear limit and its relation to flavor asymmetries in the QCD evolution of parton densities at three loops. As a phenomenological consequence of this new effect, and of the fact that the nucleon has non-vanishing quark valence densities, we study the perturbative generation of a strange-antistrange asymmetry s(x)-{bar s}(x) in the nucleon's sea.

Soils and sediments contaminated with toxic organic and inorganic compounds harmful to the environment and to human health are common in the urban environment. We report here on aspects of a program being carried out in the New York/New Jersey Port region to develop methods for processing dredged material from the Port to make products that are safe for introduction to commercial markets. We discuss some of the results of the program in Computational Environmental Science, Laboratory Environmental Science, and Applied Environmental Science and indicate some possible directions for future work. Overall, the program elements integrate the scientific and engineering aspects with regulatory, commercial, urban planning, local governments, and community group interests. Well-developed connections between these components are critical to the ultimate success of efforts to cope with the problems caused by contaminated urban soils and sediments.

This document describes the monitoring plan to meet the requirements for interim status groundwater monitoring at Hanford Site low-level waste burial grounds as specified by 40 CFR 265, incorporated by reference in WAC 173-303-400. The monitoring will take place at four separate low-level waste management areas in the 200-West and 200-East Areas, in the central part of the site. This plan replaces the previous monitoring plan.

A global, self-consistent estimate of sulfur dioxide emissions over the last one and a half century were estimated by using a combination of bottom-up and best available inventory methods including all anthropogenic sources. We find that global sulfur dioxide emissions peaked about 1980 and have generally declined since this time. Emissions were extrapolated to a 1{sup o} x 1{sup o} grid for the time period 1850-2000 at annual resolution with two emission height levels and by season. Emissions are somewhat higher in the recent past in this new work as compared with some comprehensive estimates. This difference is largely due to our use of emissions factors that vary with time to account for sulfur removals from fossil fuels and industrial smelting processes.

This report describes a signal processing algorithm and MATLAB software for improving spatial resolution in ultrasonic nondestructive evaluation (NDE) imaging of materials. Given a measured reflection signal and an associated reference signal, the algorithm produces an optimal least-squares estimate of the impulse response of the material under test. This estimated impulse response, when used in place of the raw reflection signal, enhances the spatial resolution of the ultrasonic measurements by removing distortion caused by the limited-bandwidth transducers and the materials under test. The theory behind the processing algorithms is briefly presented, while the reader is referred to the bibliography for details. The main focus of the report is to describe how to use the MATLAB software. Two processing examples using actual ultrasonic measurements are provided for tutorial purposes.

COGEMA Engineering Corporation (COGEMA), under a contract from CH2M Hill Hanford Group (CH2M Hill), has performed an ultrasonic nondestructive examination of selected portions of Double-Shell Tank 241-SY-101. The purpose of this examination was to provide information that could be used to evaluate the integrity of the wall of the primary tank. The requirements for the ultrasonic examination of Tank 241-SY-101 were to detect, characterize (identify, size, and locate), and record measurements made of any wall thinning, pitting, or cracks that might be present in the wall of the primary tank. Any measurements that exceed the requirements set forth in the Engineering Task Plan (ETP), RPP-17750 (Jensen 2003) and summarized on page 1 of this document, are reported to CH2M Hill and the Pacific Northwest National Laboratory (PNNL) for further evaluation. Under the contract with CH2M Hill, all data is to be recorded on disk and paper copies of all measurements are provided to PNNL for third-party evaluation. PNNL is responsible for preparing a report that describes the results of the COGEMA ultrasonic examinations.

Two and three dimensional assemblies of colloidal nanocrystals (NCs) have been of great interest during recent years [1-3]. While size-dependent optical and electronic properties of isolated particles are particularly important for fundamental research, studies of their ordered assemblies provide a transition path to the engineering of materials and devices for future practical applications. Assemblies of NCs of different materials, such as semiconductors, metals and metal oxides, have been reported in the literature during recent years [4-7]. However, perfect, crystallographic-ordered assemblies of colloidal NCs or colloidal superlattices (SLs) have been observed so far only using transmission (TEM) and scanning electron microscopy (SEM) in a very small scale of a few hundred nanometers, while macroscopic characterization and device application demonstrations have been performed mainly on amorphous, randomly packed powders of NCs [8, 9]. To make SLs available for traditional methods of characterization, they should be obtained in a sufficiently large size. For colloidal NCs soluble in variety of solvents, simple growth from solution seems to be an appropriate choice to produce SLs. In solution, NCs act as large molecules that, as shown previously [1, 8], can form nanoscale ordered assemblies by the classical Frank-Cabrerra mechanism [10] of crystal growth. It is, however, …

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The Navy railroad service line runs between Shelton, Bremerton, and Silverdale, and is used by the Navy to transfer freight to its facilities. It is also used by commercial clients to ship service items and bulk cargo for municipalities along portions of the route. Culverts of various size and construction convey streams and stormwater runoff under the railroad line. These allow transfer of water and, in some cases allow for passage of juvenile and adult salmon into waters upstream of the culverts. As part of this project, 21 culverts along a 34-mile reach (Shelton to Bremerton) of this railroad were surveyed to evaluate their function and ability to allow salmon to utilize the streams. The culverts and attached watersheds were evaluated using criteria developed by the Washington Department of Fish and Wildlife to assign a Priority Index (PI) to barriers present on each fish-bearing stream. The PI is a relative numeric rating indicator, assigned using consistent criteria related to the degree of potential habitat gained by removing barriers and improving the function of the watershed. Of the 21 culverts evaluated, five were found to be complete fish-passage barriers and six were found to be partial barriers, primarily to juvenile salmon. …

The 27 GPa pressure-induced epsilon-phi phase transition in HMX is explored using the Isentropic Compression Experiment (ICE) technique at the Sandia National Laboratories Z-machine facility. Our data indicate that this phase transition is sluggish and if it does occur to any extent under the time scales (200-500 ns) and strain rates (5 x 10{sup 5}) typical of ICE loading conditions, the amount of conversion is small.

A distributed memory message-passing parallel implementation of a finite-volume discretization of the primitive equations in the Community Atmosphere Model is presented. Due to the data dependencies resulting from the polar singularity of the latitude-longitude coordinate system, it is necessary to employ two separate domain decompositions within the dynamical core. Data must be periodically redistributed between these two decompositions. In addition, the domains contain halo regions that cover the nearest neighbor data dependencies. A combination of several techniques, such as one-sided communication and multithreading, are presented to optimize data movements. The resulting algorithm is shown to scale to very large machine configurations, even for relatively coarse resolutions.

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Under anaerobic conditions and at circumneutral pH, cells of the widely-distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated to nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium.