Here we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen gels. Epithelial cells are seeded into the cavities and covered with a second layer of collagen. The cells reorganize into hollow tissues corresponding to the geometry of the cavities. Patterned tissue arrays can be produced in 3-4 h and will undergo morphogenesis over the following one to three days. The protocol can easily be adapted to study a variety of tissues and aspects of normal and neoplastic development.

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.

In June 2004, the Demonstration Bulk Vitrification System (DBVS) was initiated with the intent to design, construct, and operate a full-scale bulk vitrification pilot-plant to treat low-activity tank waste from Hanford Tank 241-S-109. The DBVS facility uses In-Container Vitrification{trademark} (ICV{trademark}) at the core of the treatment process. The basic process steps combine liquid low-activity waste (LAW) and glassformers; dry the mixture; and then vitrify the mixture in a batch feed-while-melt process in a refractory lined steel container. Off-gases are processed through a state-of-the-art air pollution control system including sintered-metal filtration, thermal oxidation, acid gas scrubbing, and high-efficiency particulate air (HEPA) and high-efficiency gas adsorber (HEGA) filtration. Testing has focused on development and validation of the waste dryer, ICV, and sintered-metal filters (SMFs) equipment, operations enhancements, and glass formulation. With a parallel testing and design process, testing has allowed improvements to the DBVS equipment configuration and operating methodology, since its original inception. Design improvements include optimization of refractory panels in the ICV, simplifying glassformer addition equipment, increasing the number of waste feed chutes to the ICV, and adding capability for remote clean-out of piping, In addition, the U.S. Department of Energy (DOE) has provided an independent review of the entire DBVS …

When direct reactions populate highly excited, unbound configurations in the residual nucleus, the nucleus may further evolve into a compound nucleus. Alternatively, the residual system may decay by emitting particles into the continuum. Understanding the relative weights of these two processes as a function of the angular momentum and parity deposited in the nucleus is important for the surrogate-reaction technique. A particularly interesting case is compound-nucleus formation via the (d, p) reaction, which may be a useful tool for forming compound nuclei off the valley of stability in inverse-kinematics experiments. We present here a study of the compound formation probability for a closely-related direct reaction, direct-semidirect radiative neutron capture.

The Fast Ignition (FI) concept for Inertial Confinement Fusion (ICF) has the potential to provide a significant advance in the technical attractiveness of Inertial Fusion Energy (IFE) reactors. FI differs from conventional 'central hot spot' (CHS) target ignition by using one driver (laser, heavy ion beam or Z-pinch) to create a dense fuel and a separate ultra-short, ultra-intense laser beam to ignite the dense core. FI targets can burn with {approx} 3X lower density fuel than CHS targets, resulting in (all other things being equal) lower required compression energy, relaxed drive symmetry, relaxed target smoothness tolerances, and, importantly, higher gain. The short, intense ignition pulse that drives this process interacts with extremely high energy density plasmas; the physics that controls this interaction is only now becoming accessible in the lab, and is still not well understood. The attraction of obtaining higher gains in smaller facilities has led to a worldwide explosion of effort in the studies of FI. In particular, two new US facilities to be completed in 2009/2010, OMEGA/OMEGA EP and NIF-ARC (as well as others overseas) will include FI investigations as part of their program. These new facilities will be able to approach FI conditions much more closely …

MINOS (Main Injector Neutrino Oscillation Search), is a long baseline neutrino experiment designed to search for neutrino oscillations using two detectors at Fermi National Accelerator Laboratory, IL (Near Detector) and Soudan, MN (Far Detector). It will study {nu}{sub {mu}} {yields} {nu}{sub {tau}} oscillations and make a measurement on the oscillation parameters, {Delta}m{sub 23}{sup 2} and sin{sup 2} 2{theta}{sub 23}, via a {nu}{sub {mu}} beam made at Fermilab. Charge current neutrino interactions in the MINOS detectors are of three types: quasi-elastic scattering (QEL), resonance scattering (RES) and deep inelastic scattering (DIS). Of these, quasi-elastic scattering leaves the cleanest signal with just one {mu} and one proton in the final state, thus rendering the reconstruction of the neutrino energy more accurate. This thesis will outline a method to separate QEL events from the others in the two detectors and perform a calculation of {Delta}m{sub 23}{sup 2} and sin{sup 2} 2{theta}{sub 23} using those events. The period under consideration was May 2005 to February 2006. The number of observed quasi-elastic events with energies below 10 GeV was 29, where the expected number was 60 {+-} 3. A fit to the energy distribution of these events gives {Delta}m{sub 23}{sup 2} = 2.91{sub -0.53}{sup +0.49}(stat){sub …

This report provides a description of uranium contamination in the subsurface at the Hanford Site's 300 Area. The principal focus is a persistence plume in groundwater, which has not attenuated as predicted by earlier remedial investigations. Included in the report are chapters on current conditions, hydrogeologic framework, groundwater flow modeling, and geochemical considerations. The report is intended to describe what is known or inferred about the uranium contamination for the purpose of making remedial action decisions.

The 5s-5p electric-dipole resonance transitions in highly ionized promethiumlike ions have been studied applying relativistic multi-reference Moeller-Plesset second-order perturbation theory. The transition wavelengths are determined to within 0.2 {angstrom} in the more highly charged ions, where the level degeneracies are small. For somewhat lighter ions a very large reference space was used in order to account for the many degeneracies. In order to calculate transition probabilities and lifetimes, correlation corrections have been added to the transition operator in the next order. The contributions from the higher orders of the theory, that is, frequency-dependent Breit correction, Lamb shift, and mass shifts, have been estimated. The results are used to re-assess spectroscopic data from beam-foil, electron beam ion trap, and tokamak observations.

The authors present measurements of the relative branching ratios, Dalitz plot structures and CP-asymmetry values in the three-body singly Cabibbo-suppressed decays D{sup 0} {yields} {pi}{sup -}{pi}{sup +}{pi}{sup 0} and D{sup 0} {yields} K{sup -}K{sup +}{pi}{sup 0} using data collected by the BABAR detector at the PEP-II asymmetric-energy ring at SLAC. The author applies the results of the D{sup 0} {yields} {pi}{sup -}{pi}{sup +}{pi}{sup 0} analysis to extracting CP-violation parameters related to the CKM angle {gamma} (or {phi}{sub 3}) using the decay B{sup -} {yields} D{sub {pi}{sup +}{pi}{sup -}{pi}{sup 0}} K{sup -}.

The Center for Extended Magnetohydrodynamic Modeling (CEMM) is developing computer simulation models for predicting the behavior of magnetically confined plasmas. Over the first phase of support from the Department of Energy’s Scientific Discovery through Advanced Computing (SciDAC) initiative, the focus has been on macroscopic dynamics that alter the confinement properties of magnetic field configurations. The ultimate objective is to provide computational capabilities to predict plasma behavior—not unlike computational weather prediction—to optimize performance and to increase the reliability of magnetic confinement for fusion energy. Numerical modeling aids theoretical research by solving complicated mathematical models of plasma behavior including strong nonlinear effects and the influences of geometrical shaping of actual experiments. The numerical modeling itself remains an area of active research, due to challenges associated with simulating multiple temporal and spatial scales. The research summarized in this report spans computational and physical topics associated with state of the art simulation of magnetized plasmas. The tasks performed for this grant are categorized according to whether they are primarily computational, algorithmic, or application-oriented in nature. All involve the development and use of the Non-Ideal Magnetohydrodynamics with Rotation, Open Discussion (NIMROD) code, which is described at http://nimrodteam.org. With respect to computation, we have tested and …

There is growing national interest in renewable energy development based on the economic, environmental, and security benefits that these resources provide. Historically, greater development of our domestic renewable energy resources has faced a number of hurdles, primarily related to cost, regulation, and financing. With the recent sustained increase in the costs and associated volatility of fossil fuels, the economics of renewable energy technologies have become increasingly attractive to investors, both large and small. As a result, new entrants are investing in renewable energy and new business models are emerging. This study surveys some of the current issues related to wind and solar photovoltaic (PV) energy project financing in the electric power industry, and identifies both barriers to and opportunities for increased investment.

This cleanup verification package documents completion of remedial action, sampling activities, and compliance with cleanup criteria for the 118-F-2 Burial Ground. This burial ground, formerly called Solid Waste Burial Ground No. 1, was the original solid waste disposal site for the 100-F Area. Eight trenches contained miscellaneous solid waste from the 105-F Reactor and one trench contained solid waste from the biology facilities.

The Commodity Credit Corporation of the U.S. Department of Agriculture (CCC/USDA) formerly operated a grain storage facility (during most of the interval 1949-1974) at Barnes, Kansas. Carbon tetrachloride contamination was initially detected in 1986 in the town's public water supply wells. In 2006-2007, the CCC/USDA conducted a comprehensive targeted investigation at and near its former property in Barnes to investigate this contamination. In November 2007, the CCC/USDA began quarterly groundwater monitoring at Barnes. The monitoring is being conducted on behalf of the CCC/USDA by Argonne National Laboratory, in accord with the recommendations made in the report for the 2006-2007 targeted investigation (Argonne 2007). The objective is to monitor the carbon tetrachloride contamination identified in the groundwater at Barnes. The sampling is presently conducted in a network of 28 individual monitoring wells at 19 distinct locations, 2 public water supply wells, and 1 private well (Figure 1.1). The results of the 2006-2007 targeted investigation demonstrated the presence of carbon tetrachloride contamination at levels slightly exceeding the Kansas Department of Health and Environment (KDHE) Tier 2 risk-based screening level of 5.0 {micro}g/L for this compound, in a plume that appears to extend from the former CCC/USDA property northwestward, toward the Barnes public …

The 100-F-26:14 waste site includes underground pipelines associated with the 116-F-5 Ball Washer Crib and remnants of process pipelines on the west side of the 105-F Building. In accordance with this evaluation, the verification sampling results support a reclassification of this site to Interim Closed Out. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

Argonne National Laboratory has been asked to review the least-cost expansion plan (LCEP) of the Jamaica Public Service Company, Ltd. (JPSCo). The material that has been initially provided to Argonne included: (1) An electronic copy of the data and results from JPSCo's running the WASP electric system expansion planning model, (2) Approximately 20 pages of a document 'JPSCo Generation Expansion Plan', marked 'DRAFT 002', date unknown, and (3) The report 'JPSCo Least Cost Generation Expansion Plans, (1999-2009)', January 1999. It was noticed that the 20 pages from the 'DRAFT 002' document were different from the January 1999 report. An explanation was provided to Argonne that the excerpt was from an earlier draft and that the review should focus on the January 1999 report. Further, the electronic copy of the WASP case did not correspond to either the January 1999 report or to the 20-page excerpt. Again, the reason for these discrepancies was that the WASP case provided to Argonne was an earlier case and not the final one that was presented in the report. Based on the review of the available material, Argonne experts have prepared and submitted to the National Investment Bank of Jamaica (NIBJ) a preliminary draft report …

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This report highlights the activities of the Physics Division of Argonne National Laboratory in 2006. The Division's programs include the operation as a national user facility of ATLAS, the Argonne Tandem Linear Accelerator System, research in nuclear structure and reactions, nuclear astrophysics, nuclear theory, investigations in medium-energy nuclear physics as well as research and development in accelerator technology. The mission of nuclear physics is to understand the origin, evolution and structure of baryonic matter in the universe--the core of matter, the fuel of stars, and the basic constituent of life itself. The Division's research focuses on innovative new ways to address this mission.

Presentation on lessons learned from the U.S. Department of Energy?s Aquatic Species Program 1978-1996 microalgae R&D activities, presented at the 2008 AFOSR Workshop in Washington, D.C.

The paper describes the generalization of the method to produce secondary particles with a low-energy and low-intensity primary beam circulating in a Storage Ring with the Emittance-Recovery by Internal-Target (ERIT).

TMVOC-MP is a massively parallel version of the TMVOC code (Pruess and Battistelli, 2002), a numerical simulator for three-phase non-isothermal flow of water, gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous/fractured media. TMVOC-MP was developed by introducing massively parallel computing techniques into TMVOC. It retains the physical process model of TMVOC, designed for applications to contamination problems that involve hydrocarbon fuels or organic solvents in saturated and unsaturated zones. TMVOC-MP can model contaminant behavior under 'natural' environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted source remediation. With its sophisticated parallel computing techniques, TMVOC-MP can handle much larger problems than TMVOC, and can be much more computationally efficient. TMVOC-MP models multiphase fluid systems containing variable proportions of water, non-condensible gases (NCGs), and water-soluble volatile organic chemicals (VOCs). The user can specify the number and nature of NCGs and VOCs. There are no intrinsic limitations to the number of NCGs or VOCs, although the arrays for fluid components are currently dimensioned as 20, accommodating water plus 19 components that may be either NCGs or VOCs. Among them, NCG arrays are dimensioned as 10. The user may select …

At the end of the funding period (March 2003) for our program in ferroelectric oxide nanomaterials, we had 3 publications in print, one more had been submitted and two more were in preparation in peer-reviewed journals and invited symposia lectures had been given since starting the project in the Fall of 1999. We hired two postdoctoral fellows, Dr. Ki-Seog Chang and Dr. Wenzhong Wang. We have also trained two graduate students, Ms. Keri Williams and Ms. Bernadette Hernandez, and one undergraduate student (Mr. Michael Scancella).

Heterogeneous processes hold the key to understanding many problems in biology and atmospheric science. In particular, recent experiments have shown that heterogeneous chemistry at the surface of sea-salt aerosols plays a large role in important atmospheric processes with far reaching implications towards understanding of the fate and transport of aerosolized chemical weapons (i.e. organophosphates such as sarin and VX). Unfortunately, the precise mechanistic details of the simplest surface enhanced chemical reactions remain unknown. Understanding heterogeneous processes also has implications in the biological sciences. Traditionally, it is accepted that enzymes catalyze reactions by stabilizing the transition state, thereby lowering the free energy barrier. However, recent findings have shown that a multitude of phenomena likely contribute to the efficiency of enzymes, such as coupled protein motion, quantum mechanical tunneling, or strong electrostatic binding. The objective of this project was to develop and validate a single computational framework based on first principles simulations using tera-scale computational resources to answer fundamental scientific questions about heterogeneous chemical processes relevant to atmospheric chemistry and biological sciences.

We identify a third image in the unique quasar lens SDSS J1029+2623, the second known quasar lens produced by a massive cluster of galaxies. The spectrum of the third image shows similar emission and absorption features, but has a redder continuum than the other two images which can be explained by differential extinction or microlensing. We also identify several lensed arcs. Our observations suggest a complicated structure of the lens cluster at z {approx} 0.6. We argue that the three lensed images are produced by a naked cusp on the basis of successful mass models, the distribution of cluster member galaxies, and the shapes and locations of the lensed arcs. Lensing by a naked cusp is quite rare among galaxy-scale lenses but is predicted to be common among large-separation lensed quasars. Thus the discovery can be viewed as support for an important theoretical prediction of the standard cold dark matter model.

Pyridine hydrogenation in the presence of a surface monolayer consisting of cubic Pt nanoparticles stabilized by tetradecyltrimethylammonium bromide (TTAB) was investigated by sum frequency generation (SFG) vibrational spectroscopy using total internal reflection (TIR) geometry. TIR-SFG spectra analysis revealed that a pyridinium cation (C{sub 5}H{sub 5}NH{sup +}) forms during pyridine hydrogenation on the Pt nanoparticle surface, and the NH group in the C{sub 5}H{sub 5}NH{sup +} cation becomes more hydrogen bound with the increase of the temperature. In addition, the surface coverage of the cation decreases with the increase of the temperature. An important contribution of this study is the in situ identification of reaction intermediates adsorbed on the Pt nanoparticle monolayer during pyridine hydrogenation.