This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 …

The design of flight control systems for high performance maneuvering reentry vehicles presents a significant challenge to the control systems designer. These vehicles typically have a much higher ballistic coefficient than crewed vehicles like as the Space Shuttle or proposed crew return vehicles such as the X-38. Moreover, the missions of high performance vehicles usually require a steeper reentry flight path angle, followed by a pull-out into level flight. These vehicles then must transit the entire atmosphere and robustly perform the maneuvers required for the mission. The vehicles must also be flown with small static margins in order to perform the required maneuvers, which can result in highly nonlinear aerodynamic characteristics that frequently transition from being aerodynamically stable to unstable as angle of attack increases. The control system design technique of dynamic inversion has been applied successfully to both high performance aircraft and low beta reentry vehicles. The objective of this study was to explore the application of this technique to high performance maneuvering reentry vehicles, including the basic derivation of the dynamic inversion technique, followed by the extension of that technique to the use of tabular trim aerodynamic models in the controller. The dynamic inversion equations are developed for …

This report contains the groundwater and surface water monitoring data that were obtained during calendar year (CY) 2004 at the U.S. Department of Energy (DOE) Y-12 National Security Complex (hereafter referenced as Y-12) on the DOE Oak Ridge Reservation (ORR) in Oak Ridge, Tennessee. The CY 2004 monitoring data were obtained from groundwater and surface water sampling locations in three hydrogeologic regimes at Y-12 (Figure A.1). The Bear Creek Hydrogeologic Regime (Bear Creek Regime) encompasses a section of Bear Creek Valley (BCV) between the west end of Y-12 and the west end of the Bear Creek Watershed (directions are in reference to the Y-12 grid system). The Upper East Fork Poplar Creek Hydrogeologic Regime (East Fork Regime) encompasses the Y-12 industrial facilities and support structures in BCV. The Chestnut Ridge Hydrogeologic Regime (Chestnut Ridge Regime) encompasses a section of Chestnut Ridge south of Y-12. The CY 2004 monitoring data were obtained under the Y-12 Groundwater Protection Program (GWPP) managed by BWXT Y-12, L.L.C. (BWXT) and several monitoring programs managed by Bechtel Jacobs Company LLC (BJC). Data contained in this report meet applicable requirements of DOE Order 450.1 (Environmental Protection Program) regarding evaluation of groundwater and surface water quality in areas: …

This report examines the problem of an antenna radiating from a cylindrical hole in the earth and the subsequent far-zone field produced in the upper air half space. The approach used for this analysis was to first examine propagation characteristics along the hole for surrounding geologic material properties. Three cases of sand with various levels of moisture content were considered as the surrounding material to the hole. For the hole diameters and sand cases examined, the radiation through the earth medium was found to be the dominant contribution to the radiation transmitted through to the upper half-space. In the analysis presented, the radiation from a vertical and a horizontal dipole source within the hole is used to determine a closed-form expression for the radiation in the earth medium which represents a modified element factor for the source and hole combination. As the final step, the well-known results for a dipole below a half space, in conjunction with the use of Snell's law to transform the modified element factor to the upper half space, determine closed-form expressions for the far-zone radiated fields in the air region above the earth.

In October of 2003 experts involved in various aspects of homeland security from the Pacific region met to engage in a free-wheeling discussion and brainstorming (a 'fest') on the role that technology could play in winning the war on terrorism in the Pacific region. The result was a concise and relatively thorough definition of the terrorism problem in the Pacific region, emphasizing the issues unique to Island nations in the Pacific setting, along with an action plan for developing working demonstrations of advanced technological solutions to these issues. Since PacFest 2003, the maritime dimensions of the international security environment have garnered increased attention and interest. To this end, PacFest 2004 sought to identify gaps and enabling technologies for maritime domain awareness and responsive decision-making in the Asia-Pacific region. The PacFest 2004 participants concluded that the technologies and basic information building blocks exist to create a system that would enable the Pacific region government and private organizations to effectively collaborate and share their capabilities and information concerning maritime security. The proposed solution summarized in this report integrates national environments in real time, thereby enabling effective prevention and first response to natural and terrorist induced disasters through better use of national and …

This Habitat Evaluation Procedure (HEP) study was performed to determine baseline habitat units on the Oxbow Conservation Area in Grant County, Oregon. The evaluation is a required part of the Memorandum of Agreement between the Confederated Tribes of the Warm Springs and Bonneville Power Administration (BPA) relating to the acquisition and management of the Oxbow Conservation Area. The HEP team was comprised of individuals from the Washington Department of Fish and Wildlife and the Confederated Tribes of the Warm Springs Reservation of Oregon. The survey was conducted using the following HEP evaluation models for key species: black-capped chickadee (Poecile atricapilla), mallard (Anas platyrhynchos), mink (Mustela vison), western meadowlark (Sturnella neglecta), white-tailed deer (Odocoileus virginiana), and yellow warbler (Dendroica petechia). Cover types used in this survey were conifer forest, irrigated meadow, riparian meadow, upland meadow, riparian shrub, upland shrub, and mine tailings. The project generated 701.3 habitat units for mitigation crediting purposes. Results for each HEP species are: (1) Black-capped chickadee habitat was good, with only isolated areas lacking snags or having low tree canopy cover. (2) Mallard habitat was poor in upland meadows and marginal elsewhere due to a lack of herbaceous/shrub cover and low herbaceous height. (3) Mink habitat …

None

To assess the relationship of weekly walking distance to percentiles of adiposity in elders (age {ge} 75 years), seniors (55 {le} age <75 years), middle-age men (35 {le} age <55 years), and younger men (18 {le} age <35 years old). Cross-sectional analyses of baseline questionnaires from 7,082 male participants of the National Walkers Health Study. The walkers BMIs were inversely and significantly associated with walking distance (kg/m{sup 2} per km/wk) in elders (slope {+-} SE: -0.032 {+-} 0.008), seniors (-0.045 {+-} 0.005), and middle-aged men (-0.037 {+-} 0.007), as were their waist circumferences (-0.091 {+-} 0.025, -0.045 {+-} 0.005, and -0.091 {+-} 0.015 cm per km/wk, respectively), and these slopes remained significant when adjusted statistically for reported weekly servings of meat, fish, fruit, and alcohol. The declines in BMI associated with walking distance were greater at the higher than lower percentiles of the BMI distribution. Specifically, compared to the decline at the 10th BMI percentile, the decline in BMI at the 90th percentile was 5.1-fold greater in elders, 5.9-fold greater in seniors, and 6.7-fold greater in middle-age men. The declines in waist circumference associated with walking distance were also greater among men with broader waistlines. Exercise-induced weight loss (or self-selection) …

Ion mobility spectrometry (IMS) is recognized as one of the most sensitive and versatile techniques for the detection of trace levels of organic vapors. IMS is widely used for detecting contraband narcotics, explosives, toxic industrial compounds and chemical warfare agents. Increasing threat of terrorist attacks, the proliferation of narcotics, Chemical Weapons Convention treaty verification as well as humanitarian de-mining efforts has mandated that equal importance be placed on the analysis time as well as the quality of the analytical data. (1) IMS is unrivaled when both speed of response and sensitivity has to be considered. (2) With conventional (signal averaging) IMS systems the number of available ions contributing to the measured signal to less than 1%. Furthermore, the signal averaging process incorporates scan-to-scan variations decreasing resolution. With external second gate Fourier Transform ion mobility spectrometry (FT-IMS), the entrance gate frequency is variable and can be altered in conjunction with other data acquisition parameters to increase the spectral resolution. The FT-IMS entrance gate operates with a 50% duty cycle and so affords a 7 to 10-fold increase in sensitivity. Recent data on high explosives are presented to demonstrate the parametric optimization in sensitivity and resolution of our system.

On July 13, 2004, the Habitat Evaluation Procedure (HEP) was used to determine baseline habitat suitability on the Calispell Creek property, an acquisition completed by the Kalispel Tribe of Indians in February 2004. Evaluation species and appropriate models include Canada goose, mallard, muskrat, yellow warbler, and white-tailed deer. Habitat Suitability Index (HSI) values were visually estimated and agreed upon by all HEP team members. The Calispell Creek Project provides a total of 138.17 Habitat Units (HUs) for the species evaluated. Emergent wetland habitat provides 5.16 HUs for mallard and muskrat. Grassland provides 132.02 HUs for mallard and Canada goose. Scrub-shrub vegetation provides 0.99 HUs for yellow warbler and white-tailed deer. The objective of using HEP at the Calispell Creek Project and other protected properties is to document the quality and quantity of available habitat for selected wildlife species. In this way, HEP provides information on the relative value of the same area at future points in time so that the effect of management activities on wildlife habitat can be quantified. When combined with other tools, the baseline HEP will be used to determine the most effective on-site management, restoration, and enhancement actions to increase habitat suitability for targeted species. The …

This document presents the mathematical theory implemented in the CFEST (Coupled Flow, Energy, and Solute Transport) simulator. The simulator is a three-dimensional finite element model that can be used for evaluating flow and solute mass transport. Although the theory for thermal transport is presented in this guide, it has not yet been fully implemented in the simulator. The flow module is capable of simulating both confined and unconfined aquifer systems, as well as constant and variable density fluid flows. For unconfined aquifers, the model uses a moving boundary for the water table, deforming the numerical mesh so that the uppermost nodes are always at the water table. For solute transport, changes in concentration of a single dissolved chemical constituent are computed for advective and hydrodynamic transport, linear sorption represented by a retardation factor, and radioactive decay. Once fully implemented, transport of thermal energy in the groundwater and solid matrix of the aquifer can also be used to model aquifer thermal regimes. Mesh construction employs “collapsible”, hexahedral finite elements in a three-dimensional coordinate system. CFEST uses the Galerkin finite element method to convert the partial differential equations to algebraic form. To solve the coupled equations for momentum, solute and heat transport, …

A short model of asymmetric force free magnet with single beam aperture was tested at Fermilab together with the excitation test of VLHC transmission line magnet. The design concept of asymmetric force free superconducting magnet was verified by the test. The testing reached up to 104 kA current and no indication of force imbalance was observed. Since the model magnet length was only 10cm, A 0.75m model was constructed and tested at KEK with low current to ensure the validity of the design. The cool down and the excitation at KEK were also successful finding very small thermal contraction of the conductor and reasonable field homogeneity.

A search for the Standard Model Higgs boson was carried out in WH {yields} {ell}{nu}b{bar b} process in p{bar p} collisions at a center of mass energy of 1.96 TeV, where W, H, {ell}, {nu}, b and p denote either a W{sup +} or W{sup -} boson, Higgs boson, lepton (electron or muon), neutrino, bottom quark and proton, respectively. The data were collected with the Collider Detector at Fermilab from February 2002 to August 2004. The corresponding integrated luminosity is 319 pb{sup -1}. We select events containing a single high-p{sub T} electron or muon, a large imbalance of the total transverse energy from a neutrino and two b quark jets. The main backgrounds are the W + light flavor/gluon jets and W + heavy flavor jets processes. Requiring the secondary vertex b-tagging enables us to reject the W + light flavor/gluon jets events effectively. After all event selections, they observe 187 events which is in agreement with the Standard Model background expectation of 175.2 {+-} 26.3 events, and there is no significant excess originating from the Higgs boson in the reconstructed dijet invariant mass distribution. They thus set a 95% confidence level upper limit on the production cross section times …

Several nuclear weapons programs have or are pursuing the implementation of multi-unit operations for tasks such as disassembly and inspection, and rebuild. A multi-unit operation is interpreted to mean the execution of nuclear explosive operating procedures in a single facility by two separate teams of technicians. The institution of a multi-unit operations program requires careful consideration of the tools, resources, and environment provided to the technicians carrying out the work. Therefore, a systematic approach is necessary to produce safe, secure, and reliable processes. In order to facilitate development of a more comprehensive multi-unit operations program, the current work details categorized issues that should be addressed prior to the implementation of multi-unit operations in a given weapons program. The issues have been organized into the following categories: local organizational conditions, work process flow/material handling/workplace configuration, ambient environmental conditions, documented safety analysis, and training.

Not all industrial facilities have the staff or theopportunity to perform a detailed audit of their operations. The lack ofknowledge of energy efficiency opportunities provides an importantbarrier to improving efficiency. Benchmarking programs in the U.S. andabroad have shown to improve knowledge of the energy performance ofindustrial facilities and buildings and to fuel energy managementpractices. Benchmarking provides a fair way to compare the energyintensity of plants, while accounting for structural differences (e.g.,the mix of products produced, climate conditions) between differentfacilities. In California, the winemaking industry is not only one of theeconomic pillars of the economy; it is also a large energy consumer, witha considerable potential for energy-efficiency improvement. LawrenceBerkeley National Laboratory and Fetzer Vineyards developed the firstbenchmarking tool for the California wine industry called "BEST(Benchmarking and Energy and water Savings Tool) Winery". BEST Wineryenables a winery to compare its energy efficiency to a best practicereference winery. Besides overall performance, the tool enables the userto evaluate the impact of implementing efficiency measures. The toolfacilitates strategic planning of efficiency measures, based on theestimated impact of the measures, their costs and savings. The tool willraise awareness of current energy intensities and offer an efficient wayto evaluate the impact of future efficiency measures.

A new type of global shear Alfvén Eigenmode is found in tokamak plasmas where the mode localization is in the region intersecting the Alfvén continuum. The eigenmode is formed by the coupling of two solutions from two adjacent gaps (akin to potential wells) in the shear Alfvén continuum. For tokamak plasmas with reversed magnetic shear it is shown that the toroidiciy-induced solution tunnels through the continuum to match the ellipticity-induced Alfvén eigenmode (TAE and EAE, respectively) so that the resulting solution is continuous at the point of resonance with the continuum. The existence of these Double Gap Alfvén Eigenmodes (DGAEs) allows for potentially new ways of coupling edge fields to the plasma core in conditions where the core region is conventionally considered inaccessible. Implications include new approaches to heating and current drive in fusion plasmas as well as its possible use as core diagnostic in burning plasmas.

Although remote sensing methods offer advantages for monitoring important illicit process activities, remote and stand-off technologies cannot successfully detect all important processes with the sensitivity and certainty that is desired. The main scope of the program is observables, with a primary focus on chemical signatures. A number of key process signatures elude remote or stand-off detection for a variety of reasons (e.g., heavy particulate emissions that do not propagate far enough for detection at stand-off distances, semi-volatile chemicals that do not tend to vaporize and remain in the environment near the source, etc.). Some of these compounds can provide persistent, process-specific information that is not available through remote techniques; however, the associated measurement technologies have their own set of advantages, disadvantages and technical challenges that may need to be overcome before additional signature data can be effectively and reliably exploited. The main objective of this report is to describe a process to identify high impact technology gaps for important less-than-remote detection applications. The subsequent analysis focuses on the technology development needed to enable exploitation of important process signatures. The evaluation process that was developed involves three interrelated and often conflicting requirements generation activities: • Identification of target signature chemicals with …

A validation study has been conducted for a turbulence model used to close the temporally filtered Navier Stokes (TFNS) equations. A turbulence model was purposely built to support fire simulations under the Accelerated Strategic Computing (ASC) program. The model was developed so that fire transients could be simulated and it has been implemented in SIERRA/Fuego. The model is validated using helium plume data acquired for the Weapon System Certification Campaign (C6) program in the Fire Laboratory for Model Accreditation and Experiments (FLAME). The helium plume experiments were chosen as the first validation problem for SIERRA/Fuego because they embody the first pair-wise coupling of scalar and momentum fields found in fire plumes. The validation study includes solution verification through grid and time step refinement studies. A formal statistical comparison is used to assess the model uncertainty. The metric uses the centerline vertical velocity of the plume. The results indicate that the simple model is within the 95% confidence interval of the data for elevations greater than 0.4 meters and is never more than twice the confidence interval from the data. The model clearly captures the dominant puffing mode in the fire but under resolves the vorticity field. Grid dependency of the …

Leaching studies of coal utilization byproducts (CUB) are often performed to determine the compatibility of the material in a particular end-use or disposal environment. Typically, these studies are conducted using either a batch or a fixed-bed column technique. Fixed-bed columns offer the advantage of a continuous flow of effluent that provides elution profiles with changing elution volume and pH. Unfortunately, clogs can form in fixed-bed leaching columns, either because of cementitious properties of the material itself, such as is seen for fluidized bed combustion (FBC) fly ash, or because of precipitate formation, such as can occur when a high-calcium ash is subjected to sulfate-containing leachates. Also, very fine-grained materials, such as gypsum, do not provide sufficient permeability for study in a fixed-bed column. A continuous, stirred-tank extractor (CSTX) is being used as an alternative technique that can provide the elution profile of column leaching but without the low permeability problems. The CSTX has been successfully employed in the leaching of flue gas desulfurization products that would not be sufficiently permeable under traditional column leaching conditions. The results indicate that the leaching behavior depends on a number of factors, including (but not limited to) solubility and neutralization capacity of the mineral …

The thermal hazard posed by large hydrocarbon fires is dominated by the radiative emission from high temperature soot. Since the optical properties of soot, especially in the infrared region of the electromagnetic spectrum, as well as its morphological properties, are not well known, efforts are underway to characterize these properties. Measurements of these soot properties in large fires are important for heat transfer calculations, for interpretation of laser-based diagnostics, and for developing soot property models for fire field models. This research uses extractive measurement diagnostics to characterize soot optical properties, morphology, and composition in 2 m pool fires. For measurement of the extinction coefficient, soot extracted from the flame zone is transported to a transmission cell where measurements are made using both visible and infrared lasers. Soot morphological properties are obtained by analysis via transmission electron microscopy of soot samples obtained thermophoretically within the flame zone, in the overfire region, and in the transmission cell. Soot composition, including carbon-to-hydrogen ratio and polycyclic aromatic hydrocarbon concentration, is obtained by analysis of soot collected on filters. Average dimensionless extinction coefficients of 8.4 {+-} 1.2 at 635 nm and 8.7 {+-} 1.1 at 1310 nm agree well with recent measurements in the overfire …

The synthesis of a photoswitchable polymer by grafting an azobenzene dye to methacrylate followed by polymerization is presented. The azobenzene dye undergoes a trans-cis photoisomerization that causes a persistent change in the refractive index of cast polymer films. This novel polymer was incorporated into superlattices prepared by spin casting and the optical activity of the polymer was maintained. A modified coextruder that allows the rapid production of soft matter superlattices was designed and fabricated.

Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between bound toxins, and the molecular conformational changes that occur as a result of pH lowering. In an effort to elucidate the mechanism of tetanus toxin binding and permeation through the membrane a simple yet representative model was developed that consisted of the ganglioside G{sub tlb} incorporated in a bilayer of cholesterol and DPPC (dipalmitoylphosphatidyl choline). The bilayers were stable over time yet sensitive towards the binding and activity of whole toxin. A liposome leakage study at constant pH as well as with a pH gradient, to mimic the processes of the endosome, was used to elucidate the effect of pH on the toxin's membrane binding and permeation capability. Topographic imaging of the membrane surface, via in situ tapping mode AFM, provided nanoscale characterization of the toxin's binding location and pore formation …

Macroscopic quantum states such as superconductors, Bose-Einstein condensates and superfluids are some of the most unusual states in nature. In this project, we proposed to design a semiconductor system with a 2D layer of electrons separated from a 2D layer of holes by a narrow (but high) barrier. Under certain conditions, the electrons would pair with the nearby holes and form excitons. At low temperature, these excitons could condense to a macroscopic quantum state either through a Bose-Einstein condensation (for weak exciton interactions) or a BCS transition to a superconductor (for strong exciton interactions). While the theoretical predictions have been around since the 1960's, experimental realization of electron-hole bilayer systems has been extremely difficult due to technical challenges. We identified four characteristics that if successfully incorporated into a device would give the best chances for excitonic condensation to be observed. These characteristics are closely spaced layers, low disorder, low density, and independent contacts to allow transport measurements. We demonstrated each of these characteristics separately, and then incorporated all of them into a single electron-hole bilayer device. The key to the sample design is using undoped GaAs/AlGaAs heterostructures processed in a field-effect transistor geometry. In such samples, the density of single …