Shape analysis plays an important role in many applications. In particular, in molecular biology, analyzing molecular shapes is essential to the fundamental problem of understanding how molecules interact. This project aims at developing efficient and effective algorithms to characterize and analyze molecular structures using geometric and topological methods. Two main components of this project are (1) developing novel molecular shape descriptors; and (2) identifying and representing meaningful features based on those descriptors. The project also produces accompanying (visualization) software. Results from this project (09/2006–10/2009) include the following publications. We have also set up web-servers for the software developed in this period, so that our new methods are accessible to a broader scientific community. The web sites are given below as well. In this final technical report, we first list publications and software resulted from this project. We then briefly explain the research conducted and main accomplishments during the period of this project.

With international efforts to limit anthropogenic carbon in the atmosphere, various CO{sub 2} sequestration methods have been studied by various facilities worldwide. Basalt rock in general has been referred to as potential host material for mineral carbonation by various authors, without much regard for compositional variations due to depositional environment, subsequent metamorphism, or hydrothermal alteration. Since mineral carbonation relies on the presence of certain magnesium, calcium, or iron silicates, it is necessary to study the texture, mineralogy, petrology, and geochemistry of specific basalts before implying potential for mineral carbonation. The development of a methodology for the characterization of basalts with respect to their susceptibility for mineral carbonation is proposed to be developed as part of this research. The methodology will be developed based on whole rock data, petrography and microprobe analyses for samples from the Caledonia Mine in Michigan, which is the site for a proposed small-scale demonstration project on mineral carbonation in basalt. Samples from the Keweenaw Peninsula will be used to determine general compositional trends using whole rock data and petrography. Basalts in the Keweenaw Peninsula have been subjected to zeolite and prehnite-pumpellyite facies metamorphism with concurrent native copper deposition. Alteration was likely due to the circulation of …

Methods and algorithms are developed to enable the accurate analysis of problems that exhibit interacting physical processes with uncertainties. These uncertainties can pertain either to each of the physical processes or to the manner in which they depend on each others. These problems are cast within a polynomial chaos framework and their solution then involves either solving a large system of algebraic equations or a high dimensional numerical quadrature. In both cases, the curse of dimensionality is manifested. Procedures are developed for the efficient evaluation of the resulting linear equations that advantage of the block sparse structure of these equations, resulting in a block recursive Schur complement construction. In addition, embedded quadratures are constructed that permit the evaluation of very high-dimensional integrals using low-dimensional quadratures adapted to particular quantities of interest. The low-dimensional integration is carried out in a transformed measure space in which the quantity of interest is low-dimensional. Finally, a procedure is also developed to discover a low-dimensional manifold, embedded in the initial high-dimensional one, in which scalar quantities of interest exist. This approach permits the functional expression of the reduced space in terms of the original space, thus permitting cross-scale sensitivity analysis.

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The objectives of the confirmatory activities were to provide independent contractor field data reviews and to generate independent radiological data for use by the NRC in evaluating the adequacy and accuracy of the contractor�s procedures and FSS results. ORAU reviewed ABB CE�s decommissioning plan, final status survey plan, and the applicable soil DCGLs, which were developed based on an NRC-approved radiation dose assessment. The surveys include gamma surface scans, gamma direct measurements, and soil sampling.

Summary of research carried out under Interagency Agreement DE-AI02-07ER64355 with the USDA Forest Service at the Howland Forest AmeriFlux site in central Maine. Includes a list of publications resulting in part or whole from this support.

Because of their high stopping power and fast and bright scintillation, cerium doped LSO and LYSO crystals have attracted a broad interest in the physics community pursuing precision electromagnetic calorimeter for future high energy physics experiments. Their excellent radiation hardness against gamma-rays, neutrons and charged hadrons also makes them a preferred material for calorimeters to be operated in a severe radiation environment, such as the HL-LHC. An effort was made at SIPAT to grow 25 X{sub 0} (28 cm) long LYSO crystals for high energy physics applications. In this paper, the optical and scintillation properties and its radiation hardness against gamma-ray irradiations up to 1 Mrad are presented for the first 2.5 X 2.5 X 28 cm LYSO sample. An absorption band was found at the seed end of this sample and three other 20 cm long samples, which was traced back to a bad seed crystal used in the corresponding crystal growth process. Significant progresses in optical and scintillation properties were achieved for large size LYSO crystals after eliminating this absorption band.

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To address the {sup 65}Zn contamination issue in the TEF, a multi-task experimental program was initiated. The first experimental task was completed and is reported in Ref. 1. The results of the second experimental task are reported here. This task examined the effect of filter temperature on trapping efficiency and deposit morphology. Based on the first experimental tasks that examined filter pore size and trapping efficiency, stainless steel filter media with a 20 {micro}m pore size was selected. A series of experiments using these filters was conducted during this second task to determine the effect of filter temperature on zinc vapor trapping efficiency, adhesion and morphology. The tests were conducted with the filters heated to 60, 120, and 200 C; the zinc source material was heated to 400 C for all the experiments to provide a consistent zinc source. The samples were evaluated for mass change, deposit adhesion and morphology. As expected from the physical vapor deposition literature, a difference in deposit morphology and appearance was observed between the three filter temperatures. The filter held at 60 C had the largest average mass gain while the 120 and 200 C filters exhibited similar but lower weight gains. The standard deviations …

This is a feasibility study of using a modern Graphics Processing Unit (GPU) to parallelize the accelerator particle tracking code. To demonstrate the massive parallelization features provided by GPU computing, a simplified TracyGPU program is developed for dynamic aperture calculation. Performances, issues, and challenges from introducing GPU are also discussed. General purpose Computation on Graphics Processing Units (GPGPU) bring massive parallel computing capabilities to numerical calculation. However, the unique architecture of GPU requires a comprehensive understanding of the hardware and programming model to be able to well optimize existing applications. In the field of accelerator physics, the dynamic aperture calculation of a storage ring, which is often the most time consuming part of the accelerator modeling and simulation, can benefit from GPU due to its embarrassingly parallel feature, which fits well with the GPU programming model. In this paper, we use the Tesla C2050 GPU which consists of 14 multi-processois (MP) with 32 cores on each MP, therefore a total of 448 cores, to host thousands ot threads dynamically. Thread is a logical execution unit of the program on GPU. In the GPU programming model, threads are grouped into a collection of blocks Within each block, multiple threads share the …

The ultimate goal of batch-melting studies, laboratory-scale, large-scale, or mathematical modeling is to increase the rate of glass processing in an energy-efficient manner. Mathematical models are not merely an intermediate step between laboratory-scale and large-scale studies, but are also an important tool for assessing the responses of melters to vast combinations of process parameters. In the simplest melting situation considered in this study, a cold cap of uniform thickness rests on a pool of molten glass from which it receives a steady uniform heat flux. Thus, as the feed-to-glass conversion proceeds, the temperature, velocity, and extent of feed reactions are functions of the position along the vertical coordinate, and these functions do not vary with time. This model is used for the sensitivity analyses on the effects of key parameters on the cold-cap behavior.

The National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory (LLNL) in Livermore, CA, is a Nd:Glass laser facility capable of producing 1.8 MJ and 500 TW of ultraviolet light. This world's most energetic laser system is now operational with the goals of achieving thermonuclear burn in the laboratory and exploring the behavior of matter at extreme temperatures and energy densities. By concentrating the energy from its 192 extremely energetic laser beams into a mm{sup 3}-sized target, NIF can produce temperatures above 100 million K, densities of 1,000 g/cm{sup 3}, and pressures 100 billion times atmospheric pressure - conditions that have never been created in a laboratory and emulate those in the interiors of planetary and stellar environments. On September 29, 2010, NIF performed the first integrated ignition experiment which demonstrated the successful coordination of the laser, the cryogenic target system, the array of diagnostics and the infrastructure required for ignition. Many more experiments have been completed since. In light of this strong progress, the U.S. and the international communities are examining the implication of achieving ignition on NIF for inertial fusion energy (IFE). A laser-based IFE power plant will require a repetition rate of 10-20 Hz and a …

Laser evolution and plasma wave excitation by a relativistically-intense short-pulse laser in underdense plasma are investigated in the broad pulse limit, including the effects of pulse steepening, frequency red-shifting, and energy depletion. The nonlinear plasma wave phase velocity is shown to be significantly lower than the laser group velocity and further decreases as the pulse propagates owing to laser evolution. This lowers the thresholds for trapping and wavebreaking, and reduces the energy gain and efficiency of laser-plasma accelerators that use a uniform plasma profile.

Objective: This project seeks to improve the application of noble gas isotope studies to multiphase fluid processes in the Earth's crust by (1) identifying the important noble gas carrier phases in sediments to address the processes that have led to the observed enrichment and depletion patterns in sedimentary rocks and fluids, (2) examine the mechanisms by which such noble gas patterns are acquired, trapped and subsequently released to mobile crustal fluids, and (3) evaluate the time and length scales for the transport of noble gas components, such as radiogenic 4He, through the continental crust.. Project Description: Sedimentary rocks and oil field gases typically are enriched in heavy noble gases: Xe/Ar ratios of ~10-10,000 times the ratio in air have been observed that cannot be explained by adsorption hypotheses. Laboratory experiments designed to isolate sedimentary phases for noble gas analysis are conducted to identify the carrier phase(s). It has been observed that radiogenic 4He accumulates in confined aquifer waters at rates that exceed the rate of local production and approaching the whole crustal production rate. A literature evaluation of 4He, 3He crustal fluxes is being conducted to evaluate crustal scale mass transport in terms of the rate, mechanisms, temporal and spatial …

This was a four year grant commencing October 1, 2003 and finishing September 30, 2007. The funding was primarily used to support the work of the Principal Investigator, who collaborated with Profs. Scott Parker and John Cary at U. Colorado, and with two students, N. Xiang and J. Cheng also of U. Colorado. The technical accomplishments of this grant can be found in the publications listed in the final Section here. The main accomplishments of the grant work were: (1) Development and implementation of time-implicit two-fluid simulation methods in collaboration with the NIMROD team; and (2) Development and testing of a new time-implicit delta-f, energy-conserving method The basic two-fluid method, with many improvements is used in present NIMROD calculations. The energy-conserving delta-f method is under continuing development under contract between Coronado Consulting, a New Mexico sole proprietorship and the Oak Ridge National Laboratory.

The purpose of this report is to provide a concise but comprehensive overview of Atmospheric Radiation Measurement Climate Research Facility instrumentation status. The report is divided into the following five sections: (1) new instrumentation in the process of being acquired and deployed, (2) field campaigns, (3) existing instrumentation and progress on improvements or upgrades, (4) proposed future instrumentation, and (5) Small Business Innovation Research instrument development.

The motivation for the current study is to evaluate the dynamic loading response of an inert mock explosive material used to replicate the physical and mechanical properties of LX-17-1 and PBX 9502 insensitive high explosives. The evaluation of dynamic material parameters is needed for predicting the deformation behavior including the onset of failure and intensity of fragmentation resulting from high velocity impact events. These parameters are necessary for developing and validating physically based material constitutive models that will characterize the safety and performance of energetic materials. The preliminary study uses a reverse Taylor impact configuration that was designed to measure the dynamic behavior of the explosive mock up to and including associated fragmentation. A stationary rod-shaped specimen was impacted using a compressed-gas gun by accelerating a rigid steel anvil attached to a sabot. The impact test employed high-speed imaging and velocity interferometry diagnostics for capturing the transient deformation of the sample at discrete times. Once established as a viable experimental technique with mock explosives, future studies will examine the dynamic response of insensitive high explosives and propellants.

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With the long-term goal in mind of investigating if one could possibly design a 'universal solid-sample comminution technique' for debris and rubble, we have studied pulsed-laser ablation of solid samples that were contained within a surrounding fluid. Using pulses with fluences between 2 J and 0.3 J, wavelengths of 351 and 527 nm, and samples of rock, concrete, and red brick, each submerged in water, we have observed conditions in which {micro}m-scale particles can be preferentially generated in a controlled manner, during the laser ablation process. Others have studied laser peening of metals, where their attention has been to the substrate. Our study uses non-metallic substrates and analyzes the particles that are ablated from the process. The immediate impact of our investigation is that laser-comminution portion of a new systems concept for chemical analysis has been verified as feasible.

This thesis describes a search for singly produced top quarks via an electroweak vertex in head-on proton-antiproton collisions at a center of mass energy of √s = 1.96 TeV. The analysis uses a total of 2.3 fb^-1 of data collected with the D0 detector at Fermilab, corresponding to two different run periods of the Tevatron collider. Two channels contribute to single top quark production at the Tevatron, the s-channel and the t-channel. In the s-channel, a virtual W boson is produced from the aniquilation of a quark and an antiquark and a top and a bottom quarks are produced from the W decay. The top quark decays almost exclusively into a W boson and a bottom quark. Final states are considered in which the W boson decays leptonically into an electron or a muon plus a neutrino. Thus, at the detector level, the final state characterizing the s-channel contains one lepton, missing energy accounting for the neutrino, and two jets from the two bottom quarks. In the t-channel, the final state has an additional jet coming from a light quark. Clearly, a precise reconstruction of the events requires a precise measurement of the energy of the jets. A multivariate technique, …

A set of the electrostatic toroidal gyrokinetic Vlasov equation and the Poisson equation, which explicitly includes the polarization drift, is derived systematically by using Lie-transform method. The polarization drift is introduced in the gyrocenter equations of motion, and the corresponding polarization density is derived. Contrary to the wide-spread expectation, the inclusion of the polarization drift in the gyrocenter equations of motion does not affect the expression for the polarization density significantly. This is due to modification of the gyrocenter phase-space volume caused by the electrostatic potential [T. S. Hahm, Phys. Plasmas 3, 4658 (1996)] .

Using an RPA approximation, we have calculated the strengths of the singlet and triplet pairing interactions which arise from the exchange of spin and orbital fluctuations for a 2-orbital model of the Fe-pnictide superconductors. When the system is doped with F, the electron pockets become dominant and we find that the strongest pairing occurs in the singlet d-wave pairing and the triplet p-wave pairing channels, which compete closely. The pairing structure in the singlet d-wave channel corresponds to a superposition of near neighbor intra-orbital singlets with a minus sign phase difference between the d{sub xz} and d{sub yz} pairs. The leading pairing configuration in the triplet channel also involves a nearest neighbor intra-orbital pairing. We find that the strengths of both the singlet and triplet pairing grow, with the singlet pairing growing faster, as the onsite Coulomb interaction approaches the value where the S = 1 particle-hole susceptibility diverges.

The research described herein was undertaken to provide needed physical property descriptions of the Hanford transuranic tank sludges under conditions that might exist during retrieval, treatment, packaging and transportation for disposal. The work addressed the development of a fundamental understanding of the types of systems represented by these sludge suspensions through correlation of the macroscopic rheological properties with particle interactions occurring at the colloidal scale in the various liquid media. The results of the work have advanced existing understanding of the sedimentation and aggregation properties of complex colloidal suspensions. Bench scale models were investigated with respect to their structural, colloidal and rheological properties that should be useful for the development and optimization of techniques to process the wastes at various DOE sites.