Epigenetics refers to the study of heritable changes in genome function that occur without a change in primary DNA sequence. The 2009 Gordon Conference in Epigenetics will feature discussion of various epigenetic phenomena, emerging understanding of their underlying mechanisms, and the growing appreciation that human, animal, and plant health all depend on proper epigenetic control. Special emphasis will be placed on genome-environment interactions particularly as they relate to human disease. Towards improving knowledge of molecular mechanisms, the conference will feature international leaders studying the roles of higher order chromatin structure, noncoding RNA, repeat elements, nuclear organization, and morphogenic evolution. Traditional and new model organisms are selected from plants, fungi, and metazoans.

This Acceptance Test Procedure (ATP) provides for the inspection and testing of the new Pumping Instrumentation and Control (PIC) skid designated as ''V''. The ATP will be performed after the construction of the PIC skid in the fabrication shop.

The Advanced Light Source (ALS) at the E.O. Lawrence Berkeley National Laboratory (Berkeley Lab) of the University of California is a ''third-generation'' synchrotron radiation source optimized for highest brightness at ultraviolet and soft x-ray photon energies. It also provides world-class performance at hard x-ray photon energies. Berkeley Lab operates the ALS for the United States Department of Energy as a national user facility that is available 24 hours/day around the year for research by scientists from industrial, academic, and government laboratories primarily from the United States but also from abroad.

In this work, we investigate the effect of air convection on laser-beam pointing noise essential for the long trace profiler (LTP). We describe this pointing error with noise power density (NPD) frequency distributions. It is shown that the NPD spectra due to air convection have a very characteristic form. In the range of frequencies from {approx}0.05 Hz to {approx}0.5 Hz, the spectra can be modeled with an inverse-power-law function. Depending on the intensity of air convection that is controlled with a resistive heater of 100 to 150 mW along a one-meter-long optical path, the power index lies between 2 and 3 at an overall rms noise of {approx}0.5 to 1 microradian. The efficiency of suppression of the convection noise by blowing air across the beam optical path is also discussed. Air-blowing leads to a white-noise-like spectrum. Air blowing was applied to the reference channel of an LTP allowing demonstration of the contribution of air convection noise to the LTP reference beam. The ability to change (with the blowing technique presented) the spectral characteristics of the beam pointing noise due to air convection allows one to investigate the contribution of the convection effect, and thus make corrections to the power spectral …

The Department of Energy (DOE) currently has mercury (Hg) contaminated materials and soils at the various sites. Figure 1-1 (from http://www.ct.ornl.gov/stcg.hg/) shows the estimated distribution of mercury contaminated waste at the various DOE sites. Oak Ridge and Idaho sites have the largest deposits of contaminated materials. The majorities of these contaminated materials are soils, sludges, debris, and waste waters. This project concerns treatment of mercury contaminated soils. The technology is applicable to many DOE sites, in-particular, the Y-12 National Security Complex in Oak Ridge Tennessee and Idaho National Engineering and Environmental Laboratory (INEEL). These sites have the majority of the soils and sediments contaminated with mercury. The soils may also be contaminated with other hazardous metals and radionuclides. At the Y12 plant, the baseline treatment method for mercury contaminated soil is low temperature thermal desorption (LTTD), followed by on-site landfill disposal. LTTD is relatively expensive (estimated cost of treatment which exclude disposal cost for the collect mercury is greater than $740/per cubic yard [cy] at Y-12), does not treat any of the metal or radionuclides. DOE is seeking a less costly alternative to the baseline technology. As described in the solicitation (DE-RA-01NT41030), this project initially focused on evaluating cost-effective in-situ …

U.S. Department of Energy (DOE) used large quantities of mercury in the uranium separating process from the 1950s until the late 1980s in support of national defense. Some of this mercury, as well as other hazardous metals and radionuclides, found its way into, and under, several buildings, soil and subsurface soils and into some of the surface waters. Several of these areas may pose potential health or environmental risks and must be dealt with under current environmental regulations. DOE's National Energy Technology Laboratory (NETL) awarded a contract ''Alternative Field Methods to Treat Mercury in Soil'' to IT Group, Knoxville TN (IT) and its subcontractor NFS, Erwin, TN to identify remedial methods to clean up mercury-contaminated high-clay content soils using proven treatment chemistries. The sites of interest were the Y-12 National Security Complex located in Oak Ridge, Tennessee, the David Witherspoon properties located in Knoxville, Tennessee, and at other similarly contaminated sites. The primary laboratory-scale contract objectives were (1) to safely retrieve and test samples of contaminated soil in an approved laboratory and (2) to determine an acceptable treatment method to ensure that the mercury does not leach from the soil above regulatory levels. The leaching requirements were to meet the …

High-contrast adaptive optics systems, such as those needed to image extrasolar planets, are known to require excellent wavefront control and diffraction suppression. At the Laboratory for Adaptive Optics on the Extreme Adaptive Optics testbed, we have already demonstrated wavefront control of better than 1 nm rms within controllable spatial frequencies. Corresponding contrast measurements, however, are limited by amplitude variations, including those introduced by the micro-electrical-mechanical-systems (MEMS) deformable mirror. Results from experimental measurements and wave optic simulations of amplitude variations on the ExAO testbed are presented. We find systematic intensity variations of about 2% rms, and intensity variations with the MEMS to be 6%. Some errors are introduced by phase and amplitude mixing because the MEMS is not conjugate to the pupil, but independent measurements of MEMS reflectivity suggest that some error is introduced by small non-uniformities in the reflectivity.

We perform an analytic semi-classical quantization of the straight QCD string with one end fixed and a massless quark on the other, in the limits of orbital and radial dominant motion. Our results well approximate those of the exact numerical semi-classical quantization as well as our exact numerical canonical quantization.

This report contains citrate data for groundwaters received from the 100-N Area. On April 4, 2007, 7 water samples were received from the 100-N Area for citrate analysis. The analyses for this project were performed at the 325 building located in the 300 Area of the Hanford Site. The analyses were performed according to Pacific Northwest National Laboratory (PNNL) approved procedures. The data sets include the sample identification numbers, analytical results, estimated quantification limits (EQL) and quality control data.

This project demonstrated that treated drill cuttings derived from oil and gas operations could be used as source material for rebuilding eroding wetlands in Louisiana. Planning to supply a restoration site, drill a source well, and provide part of the funding. Scientists from southeastern Louisiana University's (SLU) Wetland Biology Department were contracted to conduct the proposed field research and to perform mesocosm studies on the SLU campus. Plans were to use and abandoned open water drill slip as a restoration site. Dredged material was to be used to create berms to form an isolated cell that would then be filled with a blend of dredged material and drill cuttings. Three elevations were used to test the substrates ability to support various alternative types of marsh vegetation, i.e., submergent, emergent, and upland. The drill cuttings were not raw cuttings, but were treated by either a dewatering process (performed by Cameron, Inc.) or by a stabilization process to encapsulate undesirable constituents (performed by SWACO, Division of Smith International).

A new narrowband active damping system for longitudinal coupled bunch (CB) modes in the Fermilab Booster has recently been installed and tested. In the past, the Booster active damper system consisted of four independent front-ends. The summed output was distributed to the 18, h=84 RF accelerating cavities via the RF fan-out system. There were several problems using the normal fan-out system to deliver the longitudinal feedback RF. The high power RF amplifiers normally operate from 37 MHz to 53 MHz whereas the dampers operate around 83MHz. Daily variations in the tuning of the RF stations created tuning problems for the longitudinal damper system. The solution was to build a dedicated narrowband, Q {approx} 10, 83MHz cavity powered with a new 3.5kW solid-state amplifier. The cavity was installed in June 2002 and testing of the amplifier and damper front-end began in August 2002. A significant improvement has been made in both operational stability and high intensity beam damping. At present there are five CB modes being damped and a sixth mode module is being built. The new damper hardware is described and data showing the suppression of the coupled-bunch motion at high intensity is presented.

This Calculation is intended to satisfy engineering requirements for maximum 60-minute precipitation amounts for 50 and 100-year return periods at and near Yucca Mountain. This data requirement is documented in the ''Interface Control Document for Support Operations to Surface Facilities Operations Functional and Organizational Interfaces'' (CRWMS M&O 1998a). These developed data will supplement the information on 0.1 hour to 6-hour (in 0.1-hour increments) probable maximum precipitation (PMP) presented in the report, ''Precipitation Design Criteria for Storm Water Management'' (CRWMS M&O 1998b). The Reference Information Base (RIB) item, Precipitation ''Characteristics for Storm Water Management'' (M09902RIB00045 .OOO), was developed based on CRWMS M&O (1998b) and will be supplemented (via revision) with the information developed in this Calculation. The ''Development Plan for the Calculation: Precipitation Characteristics for Storm Water Management'' (CRWMS M&O 2000) was prepared in accordance with AP-2.l3Q, ''Technical Product Development Planning''. This calculation was developed in accordance with AP-3.12Q, Rev. O/ICN 2.

Symmetric multiprocessor (SMP) clusters have become the prevalent computing platforms for large-scale scientific computation in recent years mainly due to their good scalability. In fact, many parallel machines being used at supercomputing centers and national laboratories are of this type. It is critical and often very difficult on such large-scale parallel computers to efficiently manage a stream of jobs, whose requirement for resources and computing time greatly varies. Understanding the characteristics of workload imposed on a target environment plays a crucial role in managing system resources and developing an efficient resource management scheme. A parallel workload is analyzed typically by studying the traces from actual production parallel machines. The study of the workload traces not only provides the system designers with insight on how to design good processor allocation and job scheduling policies for efficient resource management, but also helps system administrators monitor and fine-tune the resource management strategies and algorithms. Furthermore, the workload traces are a valuable resource for those who conduct performance studies through either simulation or analytical modeling. The workload traces can be directly fed to a trace-driven simulator in a more realistic and specific simulation experiments. Alternatively, one can obtain certain parameters that characterize the workload …

The understanding of the physical mechanisms by which important biological inhibitors control the nucleation, growth, aggregation, and phase transformation of calcium oxalate crystals at fundamental level is of importance not only to the advances in biomineralization but also to the development of stone disease therapy. Of the three phases of calcium oxalate crystalline, calcium oxalate monohydrate (COM) and dehydrate (COD) are found in the majority of stones formed in the urinary system. Only COM, a major inorganic component of kidney stones, produces adverse physiological effects to human, however. Although a great deal of research has been carried out on the modulation of nucleation, growth, aggregation, and phase transformation of calcium oxalates by biological molecules, the basic mechanism has not yet been determined due to inherent limitations of those techniques that have been utilized The invention of atomic force microscopy (AFM) has opened a new avenue for the study of the crystal growth in general. One can now probe the growth kinetics and dynamics, and morphology of crystal surfaces down to molecular levels as a typical AFM has a lateral resolution of nanometers. In this study, in situ AFM was used to monitor the COM surface under controlled growth conditions. The …

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The beam delivery system for the linear collider focuses beams to nanometer sizes at its interaction point, collimates the beam halo to provide acceptable background in the detector and has a provision for state-of-the art beam instrumentation in order to reach the ILCs physics goals. This paper describes the design details and status of the baseline configuration considered for the reference design and also lists alternatives.

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Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least …

Mineral carbonation is a promising concept for permanent CO{sub 2} sequestration due to the vast natural abundance of the raw materials and the permanent storage of CO{sub 2} in solid form as carbonates. The sequestration of CO{sub 2} through the employment of magnesium silicates--olivine and serpentine--is beyond the proof of concept stage. For the work done in this project, serpentine was chosen as the feedstock mineral due to its abundance and availability. Although the reactivity of olivine is greater than that of serpentine, physical and chemical treatments have been shown to increase greatly the reactivity of serpentine. The primary drawback to mineral carbonation is reaction kinetics. To accelerate the carbonation, aqueous processes are preferred, where the minerals are first dissolved in solution. In aqueous carbonation, the key step is the dissolution rate of the mineral, where the mineral dissolution reaction is likely to be surface-controlled. The relatively low reactivity of serpentine has warranted research into physical and chemical treatments that have been shown to greatly increase its reactivity. The use of sulfuric acid as an accelerating medium for the removal of magnesium from serpentine has been investigated. To accelerate the dissolution process, the mineral can be ground to very fine …

Reports the results of a comprehensive development and analysis of a database on irradiation hardening and embrittlement of tempered martensitic steels (TMS). Alloy specific quantitative semi-empirical models were derived for the dpa dose, irradiation temperature (ti) and test (Tt) temperature of yield stress hardening (or softening) .

OAK B188 Effects of Water Radiolysis in Water Cooled Reactors, NERI Proposal No.99-0010. The aim of this project is to develop an experiment-and-theory based model for the radiolysis of nonstandard aqueous systems like those that will be encountered in the Advance Light Water reactor. Three aspects of the radiation chemistry of aqueous systems at elevated temperatures are considered in the project: the radiation-induced reaction within the primary track and with additives, the homogeneous production of H{sub 2}O{sub 2} at high radiation doses, and the heterogeneous reaction of the radiation-induced species escaping the track. The goals outlined for Phase 1 of the program were: the compilation of information on the radiation chemistry of water at elevated temperatures, the simulation of existing experimental data on the escape yields of e{sub aq}{sup -}, OH, H{sub 2} and H{sub 2}O{sub 2} in {gamma} radiolysis at elevated temperatures, the measurement of low LET and high LET production of H{sub 2}O{sub 2} at room temperature, the compilation of information on the radiation chemistry of water-(metal) oxide interfaces, and the synthesis and characterization the heterogeneous water-oxide systems of interest.

Testing Summary Pacific Northwest National Laboratory (PNNL) has been tasked by Bechtel National Inc. (BNI) on the River Protection Project-Hanford Tank Waste Treatment and Immobilization Plant (RPP-WTP) project to perform research and development activities to resolve technical issues identified for the Pretreatment Facility (PTF). The Pretreatment Engineering Platform (PEP) was designed and constructed and is to be operated as part of a plan to respond to issue M12, “Undemonstrated Leaching Processes.” The PEP is a 1/4.5-scale test platform designed to simulate the WTP pretreatment caustic leaching, oxidative leaching, ultrafiltration solids concentration, and slurry washing processes. The PEP replicates the WTP leaching processes using prototypic equipment and control strategies. The PEP also includes non-prototypic ancillary equipment to support the core processing. Two operating scenarios are currently being evaluated for the ultrafiltration process (UFP) and leaching operations. The first scenario has caustic leaching performed in the UFP-2 ultrafiltration feed vessels (i.e., vessel UFP-VSL-T02A in the PEP and vessels UFP-VSL-00002A and B in the WTP PTF). The second scenario has caustic leaching conducted in the UFP-1 ultrafiltration feed preparation vessels (i.e., vessels UFP-VSL-T01A and B in the PEP; vessels UFP-VSL-00001A and B in the WTP PTF). In both scenarios, 19-M sodium hydroxide solution …

Pacific Northwest National Laboratory (PNNL) has been tasked by Bechtel National Inc. (BNI) on the River Protection Project-Hanford Tank Waste Treatment and Immobilization Plant (RPP-WTP) project to perform research and development activities to resolve technical issues identified for the Pretreatment Facility (PTF). The Pretreatment Engineering Platform (PEP) was designed, constructed, and operated as part of a plan to respond to issue M12, “Undemonstrated Leaching Processes.” The PEP is a 1/4.5-scale test platform designed to simulate the WTP pretreatment caustic leaching, oxidative leaching, ultrafiltration solids concentration, and slurry washing processes. The PEP replicates the WTP leaching processes using prototypic equipment and control strategies. Two operating scenarios were evaluated for the ultrafiltration process (UFP) and leaching operations. The first scenario has caustic leaching performed in the UFP-VSL-T01A/B ultrafiltration feed vessels, identified as Integrated Test A. The second scenario has caustic leaching conducted in the UFP-VSL-T02A ultrafiltration feed preparation vessel, identified as Integrated Test B. Washing operations in PEP Integrated Tests A and B were conducted successfully as per the approved run sheets. However, various minor instrumental problems occurred, and some of the process conditions specified in the run sheet were not met during the wash operations, such as filter-loop flow-rate targets not …