Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved …

I develop a formulation for Hamiltonian dynamics in an accelerator with magnets whose edges follow a spiral. I demonstrate using this Hamiltonian that a spiral FFAG can be made perfectly 'scaling'. I describe how one computes the RF phase during a rapid acceleration cycle to keep the beam at the appropriate RF phase. I examine the effect of tilting an RF cavity with respect a radial line from the center of the machine, potentially with a different angle than the spiral of the magnets. I discuss partially the effects of the finite energy jumps on the dynamics. This is a status report of work that is still incomplete.

The influence of epitaxial strain, in the form of tetragonal distortions, on the magnetic and magnetotransport properties of La{sub 0.67}Sr{sub 0.33}MnO{sub 3} thin films was studied. The tetragonal distortion (c/a ratio) was modulated through the choice of the substrate, ranging from c/a=1.007 on (001)-oriented (LaAlO{sub 3}){sub 0.3}(Sr{sub 2}AlTaO{sub 6}){sub 0.7} substrates to 0.952 on (110)-oriented GdScO{sub 3} substrates. In agreement with previous theoretical predictions, these large values of tensile strain cause the Curie temperature and the saturation magnetization to decrease, alter the temperature dependence of the resistivity and magnetoresistance, and increase the resistivity several orders of magnitude.

Hydrogen has been identified as a leading candidate to replace petroleum as part of the transition to a sustainable energy system, and major efforts are being conducted worldwide to develop the technologies and supporting activities required for this transition. In the United States, the federal research efforts are led by the U.S. Department of Energy (DOE). The U.S. DOE Hydrogen Program is an integrated inter-office program being conducted by the Office of Energy Efficiency and Renewable Energy, Office of Nuclear Energy (DOE-NE), Office of Fossil Energy and Office of Science. The primary objective of the DOE-NE Nuclear Hydrogen Initiative (NHI) is to develop the nuclear hydrogen production technologies necessary to produce hydrogen at a cost competitive with other alternative transportation fuels. The focus of the NHI is on thermochemical cycles and high temperature electrolysis. The Savannah River National Laboratory (SRNL) has been tasked with the primary responsibility to perform research and development in order to characterize, evaluate and develop the Hybrid Sulfur (HyS) thermochemical process. The HyS Process uses a sulfur dioxide depolarized electrolyzer (SDE) to split water and produce hydrogen. During FY05 and FY06, SRNL designed and conducted proof-of-concept testing for a SDE using a low temperature, PEM fuel …

The twin aspects of energy and control (or direction) are the underlying concepts. Matter and energy are closely linked, and their understanding and control will have overwhelming importance for our civilization, our planet, our science, and our technology. This importance ranges even beyond the large portfolio of BES, both because these truly significant Grand Challenges confront many other realms of science and because even partial solutions to these challenges will enrich scientists’ collective imagination and ability to solve problems with new ideas and new methods.

A Plesset-type treatment [J. Appl. Phys. 25, 96 (1954)] is used to assess the effects of contiguous density gradients at an accelerating spherical classical interface on Rayleigh-Taylor and Bell-Plesset perturbation growth. Analytic expressions are obtained that describe enhanced Rayleigh-Taylor instability growth from contiguous density gradients aligned with the acceleration and which increase the effective Atwood number of the perturbed interface. A new pathway for geometric amplification of surface perturbations on an accelerating interface with contiguous density gradients is identified. A resonance condition between the density-gradient scalelength and the radius of the interface is also predicted based on a linearized analysis of Bernoulli's equation, potentially leading to enhanced perturbation growth. Comparison of the analytic treatment with detailed two-dimensional single-mode growth-factor simulations shows good agreement for low-mode numbers where the effects of spherical geometry are most manifested.

High temperature solid oxide electrolysis cells (SOECs) offer high electrical efficiency and a potential path to large scale hydrogen production. Solid oxide technology is capable of both power generation and hydrogen production. That makes it possible for the development of a reversible solid-oxide system that can respond to market conditions to produce electricity or hydrogen on demand. New high-temperature electrolyzer cell materials are needed to enable cost-effective hydrogen production system designs based on reversible steam electrolysis. Two test methods were established for the eventual development of the reversible, durable electrode materials: the button cell test and the oxygen electrode test. The button cell test is capable of evaluating the performance and degradation of full solid oxide cells with dual atmosphere of air and hydrogen-steam. The oxygen electrode test is capable of isolating the performance and degradation of the oxygen electrode. It has higher throughput and sensitivity than the button cell test.

The overall goals of the Tank Farm Vadose Zone Project, led by CH2M HILL Hanford Group, Inc., are 1) to define risks from past and future single-shell tank farm activities, 2) to identify and evaluate the efficacy of interim measures, and 3) to aid, via collection of geochemical information and data, the future decisions that must be made by the U.S. Department of Energy (DOE) regarding the near-term operations, future waste retrieval, and final closure activities for the single-shell tank Waste Management Areas (WMAs). For a more complete discussion of the goals of the Tank Farm Vadose Zone Project, see the overall work plan, Phase 1 RCRA Facility Investigation/Corrective Measures Study Work Plan for the Single-Shell Tank Waste Management Areas (DOE 1999). Specific details on the rationale for activities performed at WMA U are found in Crumpler (2003). To meet these goals, CH2M HILL Hanford Group, Inc., asked scientists from Pacific Northwest National Laboratory (PNNL) to perform detailed analyses of vadose zone sediment collected within the U Single-Shell Tank Farm. Specifically, this report contains all the geochemical and selected physical characterization data collected on vadose zone sediment recovered from ten direct push characterization holes emplaced to investigate vadose zone contamination …

A variety of system configurations are used in North America to meet the heating and domestic hot water needs of single-family homes. This includes, for example: warm air furnaces with electric water heaters; boilers with integrated hot water coils; and boilers with 'indirect' hot water storage tanks. Integrated hydronic systems which provide both heat and hot water are more popular only in the Northeast and mid-Atlantic regions. For those making decisions about configurations of these integrated hydronic systems, including control options, little information is available concerning the annual energy cost implications of these decisions. This report presents results of a project to use a direct load emulation approach to measure the performance of hydronic systems, develop performance curves, and to provide decision tools to consumers. This is a laboratory measurement system involving direct energy input and output measurements under different load patterns. These results are then used to develop performance correlations for specific systems that can be used to predict energy use in specific applications. A wide range of system types have been tested under this project including conventional boilers with 'tankless' internal coils for domestic hot water production, boilers with indirect external storage tanks, tank type water heaters which …

After commenting briefly on the role of the typicality assumption in science, we advocate a phenomenological approach to the cosmological measure problem. Like any other theory, a measure should be simple, general, well defined, and consistent with observation. This allows us to proceed by elimination. As an example, we consider the proper time cutoff on a geodesic congruence. It predicts that typical observers are quantum fluctuations in the early universe, or Boltzmann babies. We sharpen this well-known youngness problem by taking into account the expansion and open spatial geometry of pocket universes. Moreover, we relate the youngness problem directly to the probability distribution for observables, such as the temperature of the cosmic background radiation. We consider a number of modifications of the proper time measure, but find none that would make it compatible with observation.

Eighty-nine (89) percent of the electricity supplied in the 35-county Pittsburgh region (comprising parts of the states of Pennsylvania, Ohio, West Virginia, and Maryland) is generated by coal-fired power plants making this an ideal region in which to study the effects of the fine airborne particulates designated as PM{sub 2.5} emitted by the combustion of coal. This report demonstrates that during the period from 1999-2006 (1) sufficient and extensive exposure data, in particular samples of speciated PM{sub 2.5} components from 1999 to 2003, and including gaseous co-pollutants and weather have been collected, (2) sufficient and extensive mortality, morbidity, and related health outcomes data are readily available, and (3) the relationship between health effects and fine particulates can most likely be satisfactorily characterized using a combination of sophisticated statistical methodologies including latent variable modeling (LVM) and generalized linear autoregressive moving average (GLARMA) time series analysis. This report provides detailed information on the available exposure data and the available health outcomes data for the construction of a comprehensive database suitable for analysis, illustrates the application of various statistical methods to characterize the relationship between health effects and exposure, and provides a road map for conducting the proposed study. In addition, a detailed …

A variety of surveillance operations require the ability to track vehicles over a long period of time using sequences of images taken from a camera mounted on an airborne or similar platform. In order to be able to see and track a vehicle for any length of time, either a persistent surveillance imager is needed that can image wide fields of view over a long time-span or a highly maneuverable smaller field-of-view imager is needed that can follow the vehicle of interest. The algorithm described here was designed for the persistence surveillance case. In turns out that most vehicle tracking algorithms described in the literature[1,2,3,4] are designed for higher frame rates (> 5 FPS) and relatively short ground sampling distances (GSD) and resolutions ({approx} few cm to a couple tens of cm). But for our datasets, we are restricted to lower resolutions and GSD's ({ge}0.5 m) and limited frame-rates ({le}2.0 Hz). As a consequence, we designed our own simple approach in IDL which is a deterministic, motion-guided object tracker. The object tracking relies both on object features and path dynamics. The algorithm certainly has room for future improvements, but we have found it to be a useful tool in evaluating …

This memo discusses the analysis of the high-energy x-ray distribution from a laser-induced plasma to determine the superthermal electron distribution. The methods of deconvolution outlined in I are similar to formulae derived in the literature not including and including effects due to electron stopping. In II the methods are applied to an x-ray spectrum from an Au disc irradiated by ARGUS.

This report summarizes the results of environmental surveys conducted within the corridor of a temporary haul road (''Haul Road'') to be constructed from East Tennessee Technology Park (ETTP) to the Environmental Management Waste Management Facility (EMWMF) located just west of the Y-12 National Security Complex (Y-12). Environmental surveys were conducted by natural resource experts at Oak Ridge National Laboratory who routinely assess the significance of various project activities on the Oak Ridge Reservation (ORR). ORNL assistance to the Haul Road Project included environmental assessments necessary to determine the best route for minimizing impacts to sensitive resources such as wetlands or rare plants. Once the final route was chosen, environmental surveys were conducted within the corridor to evaluate the impacts to sensitive resources that could not be avoided. The final Haul Road route follows established roads and a power-line corridor to the extent possible (Fig. 1). Detailed explanation regarding the purpose of the Haul Road and the regulatory context associated with its construction is provided in at least two major documents and consequently is not presented here: (1) Explanation of Significant Differences for the Record of Decision for the Disposal of Oak Ridge Reservation Comprehensive Environmental Response, Compensation, and Liability Act …

An investigation of fracturing in LiFePO{sub 4} particles as a function of the particle morphology and history is presented. Two types of samples, one subjected to electrochemical cycling and another to chemical delithiation are compared. We observe the formation of micro fractures parallel to low indexed lattice planes in both samples. The fracture surfaces are predominantly parallel to (100) planes in the chemically delithiated powder and (100) and (010) planes in the electrochemically cycled powder. A consideration of the threshold stresses for dislocation glide shows that particle geometry plays an important role in the observed behavior.

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container. Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 …

This report summarizes the earthquake activity at the Hanford Site a vicinty that occurred during FY 2006

Adaptive management consists in patterning human sustenancewithin the constraints of Earth and biological systems whose behavior isinherently uncertain and difficult to control. For successful adaptivemanagement, a mind-set recognizing the limitations of science isneeded.

This report gives a summary of the achievements under DOE contract No. DOE/ER/14150 during the period September 1, 1990 to December 31, 2007. This project was concerned with the molecular modeling of solid-fluid equilibrium. The focus was on understanding how solid-fluid and solid-solid phase behavior are related to molecular structure, and the research program made a seminal contribution in this area. The project led to 34 journal articles, including a comprehensive review article published in Advances in Chemical Physics. The DOE funding supported the work of 5 Ph.D. students, 2 M.S. students and 5 postdoctoral researchers.

First-order reliability methodology (FORM) is used to develop reliability-based design factors for deterministic analyses of stress corrosion cracking. The basic elements of FORM as applied to structural reliability problems are reviewed and then employed specifically to stress corrosion cracking evaluations. Failure due to stress corrosion cracking is defined as crack initiation followed by crack growth to a critical depth. The stress corrosion cracking process is thus represented in terms of a crack initiation time model and a crack growth rate model, with the crack growth rate integrated from the initiation time to the time at which the crack grows to its critical depth. Both models are described by log-normal statistical distribution functions. A procedure is developed to evaluate design factors that are applied to the mean values of the crack initiation time and the crack growth rate for specified temperature and stress conditions. The design factors, which depend on the standard deviations of the statistical distributions, are related to a target reliability, which is inversely related to an acceptable probability of failure. The design factors are not fixed, but are evaluated on a case-to-case basis for each application. The use of these design factors in a deterministic analysis assures that …

This project involved images of Titan, Neptune, and Uranus obtained using the 10-meter W.M. Keck II Telescope and its adaptive optics system. An adaptive optics system corrects for turbulence in the Earth's atmosphere by sampling the wavefront and applying a correction based on the distortion measured for a known source within the same isoplanatic patch as the science target (for example, a point source such as a star). Adaptive optics can achieve a 10-fold increase in resolution over that obtained by images without adaptive optics (for example, Saturn's largest moon Titan is unresolved without adaptive optics but at least 10 resolution elements can be obtained across the disk in Keck adaptive optics images). The adaptive optics correction for atmospheric turbulence is not perfect; a point source is converted to a diffraction-limited core surrounded by a ''halo''. This halo is roughly the size and shape of the uncorrected point spread function one would observe without adaptive optics. In order to enhance the sharpness of the Keck images it is necessary to apply a deconvolution algorithm to the data. Many such deconvolution algorithms exist such as maximum likelihood and maximum entropy. These algorithms suffer to various degrees from noise amplification and creation …

The purpose of this discussion is to indicate the threshold values for low-order detonator response by using first principles applied to pin-to-pin configurations and associated limits in pin-to-case scenarios. In addition an attempt to define the electrical environment by first principles is shown to be inadequate and indicates the need to define the electrical insult by reasonable standards. A comparison of two accepted electrical models and a combination of the extreme reported levels from both standards are used to establish an extreme set of parameters for a safety assessment. A simplification of the critical electrical insult parameters is then shown and demonstrated to provide the initial screening protocol with easily defined electrical dimensions of action integral. Action integral and the conductive material properties are the basic parameters needed to define the solid, liquid, and gas phases of the material used for detonator bridge wires. The resulting material phases are directly related to detonator response thresholds. The discussion concludes by showing the ability of ESD insults to arc from pin-to-case, the limited knowledge of the associated arc initiation process, and the modeling need for a reasonable arc resistance in pin-to-case scenarios.

The Plutonium Immobilization Program requires development of the process and plant prototypic equipment to immobilize surplus plutonium in ceramic for long-term storage. Because of the hazardous nature of plutonium, it was necessary to develop a remotely operable materials transfer system which can function within the confines of a glovebox. In support of this work at LLNL, such a material transfer system (MTS) was developed. This paper presents both the mechanical and controls parts making up this system, and includes photographs of the key components and diagrams of their assemblies, as well as a description of the control sequence used to validate the MTS capabilities.

The purpose of this calculation report is to document the thermohydrologic (TH) model calculations performed for the Supplemental Science and Performance Analysis (SSPA), Volume 1, Section 5 and Volume 2 (BSC 2001d [DIRS 155950], BSC 2001e [DIRS 154659]). The calculations are documented here in accordance with AP-3.12Q REV0 ICN4 [DIRS 154418]. The Technical Working Plan (Twp) for this document is TWP-NGRM-MD-000015 Real. These TH calculations were primarily conducted using three model types: (1) the Multiscale Thermohydrologic (MSTH) model, (2) the line-averaged-heat-source, drift-scale thermohydrologic (LDTH) model, and (3) the discrete-heat-source, drift-scale thermal (DDT) model. These TH-model calculations were conducted to improve the implementation of the scientific conceptual model, quantify previously unquantified uncertainties, and evaluate how a lower-temperature operating mode (LTOM) would affect the in-drift TH environment. Simulations for the higher-temperature operating mode (HTOM), which is similar to the base case analyzed for the Total System Performance Assessment for the Site Recommendation (TSPA-SR) (CRWMS M&O 2000j [DIRS 153246]), were also conducted for comparison with the LTOM. This Calculation Report describes (1) the improvements to the MSTH model that were implemented to reduce model uncertainty and to facilitate model validation, and (2) the sensitivity analyses conducted to better understand the influence of parameter …