DCE Bio Detection System Final Report

The DCE (DNA Capture Element) Bio-Detection System (Biohound) was conceived, designed, built and tested by PNNL under a MIPR for the US Air Force under the technical direction of Dr. Johnathan Kiel and his team at Brooks City Base in San Antonio Texas. The project was directed toward building a measurement device to take advantage of a unique aptamer based assay developed by the Air Force for detecting biological agents. The assay uses narrow band quantum dots fluorophores, high efficiency fluorescence quenchers, magnetic micro-beads beads and selected aptamers to perform high specificity, high sensitivity detection of targeted biological materials in minutes. This final report summarizes and documents the final configuration of the system delivered to the Air Force in December 200

Phase Transitions in Finite Nuclei and the Integer Nucleon Number Problem

The study of spherical-deformed ground--state phase transitions in finite nuclei as a function of N and Z is hindered by the discrete values of the nucleon number. A resolution of the integer nucleon number problem, and evidence relating to phase transitions in finite nuclei, are discussed from the experimental point of view and interpreted within the framework of the interacting boson model.Comment: 8 pages Latex + 8 figs (postscript). In Phys Rev Lett, June 199

Selective Media for Actinide Collection and Pre-Concentration: Results of FY 2006 Studies

In this work, we have investigated new materials for potential use in automated radiochemical separations. The work can be divided into three primary tasks: (1) synthesis of new ligands with high affinity for actinide ions, (2) evaluation of new materials for actinide ion affinity, and (3) computational design of advanced ligand architectures for highly selective binding of actinide ions. Ligand Synthesis Work was conducted on synthesizing Kl?ui ligand derivatives containing functionalized pendant groups on the cyclopentadienyl ring. The functionalized pendent groups would allow these ligands to be attached to organic and inorganic solid supports. This work focused on synthesizing the compound Na[Cp?Co(PO(OC2H5)2)3], where Cp?= C5H4C(O)OCH3. Synthesizing this compound is feasible, but the method used in FY 2006 produced an impure material. A modified synthetic scheme has been developed and will be pursued in FY 2007. Work was also initiated on synthesizing bicyclic diamides functionalized for binding to polymeric resins or other surfaces. Researchers at the University of Oregon are collaborators in this work. To date, this effort has focused on synthesizing and characterizing a symmetrically substituted bicyclic diamide ligand with the ?COOH functionality. Again, this synthetic effort will continue into FY 2007. Separations Material Evaluation Work was conducted in FY 2006 to provide a more extensive set of data on the selectivity and affinity of extraction chromatography resins prepared by sorption of Kl?ui ligand onto an inert macroreticular polymeric support. Consistent with previous observations, it was found that these materials strongly bind tetravalent actinides. These materials also adsorb trivalent actinides at low nitric acid concentrations, but the affinity for the trivalent actinides decreases with increasing nitric acid concentration. These materials have relatively low affinity for U(VI), but they do sorb U(VI) to a greater extent than Am(III) at [HNO3] > 0.3 M. Preliminary results suggest that the Kl?ui resins can separate Pu(IV) from sample solutions containing high concentrations of competing ions. Conceptual protocols for recovery of the Pu from the resin for subsequent analysis have been proposed, but further work is needed to perfect these techniques. Work on this subject will be continued in FY 2007. Automated laboratory equipment (in conjunction with Task 3 of the NA-22 Automation Project) will be used in FY 2007 to improve the efficiency of these experiments. The sorption of actinide ions on self-assembled monolayer on mesoporous supports materials containing diphosphonate groups was also investigated. These materials also showed a very high affinity for tetravalent actinides, and they also sorbed U(VI) fairly strongly. Computational Ligand Design An extended MM3 molecular mechanics model was developed for calculating the structures of Kl?ui ligand complexes. This laid the groundwork necessary to perform the computer-aided design of bis-Kl?ui architectures tailored for Pu(IV) complexation. Calculated structures of the Kl?ui ligand complexes [Pu(Kl?ui)2(OH2)2]2+ and [Fe(Kl?ui)2]+ indicate a ''bent'' sandwich arrangement of the Kl?ui ligands in the Pu(IV) complex, whereas the Fe(III) complex prefers a ''linear'' octahedral arrangement of the two Kl?ui ligands. This offers the possibility that two Kl?ui ligands can be tethered together to form a material with very high binding affinity for Pu(IV) over Fe(III). The next step in the design process is to use de novo molecule building software (HostDesigner) to identify potential candidate architectures

The collapse of intermediate structures?

How can we explain the rise of President Trump and the attraction of his campaign behavior before and since he took office? We argue here that the collapse of ‘intermediate structures’ has been a key factor; that the associations and groups which are building blocks of pluralistic politics have been eroded to such an extent that Trump’s personality politics have been able to take over the political stage

p-form spectra and Casimir energies on spherical tesselations

Casimir energies on space-times having the fundamental domains of semi-regular spherical tesselations of the three-sphere as their spatial sections are computed for scalar and Maxwell fields. The spectral theory of p-forms on the fundamental domains is also developed and degeneracy generating functions computed. Absolute and relative boundary conditions are encountered naturally. Some aspects of the heat-kernel expansion are explored. The expansion is shown to terminate with the constant term which is computed to be 1/2 on all tesselations for a coexact 1-form and shown to be so by topological arguments. Some practical points concerning generalised Bernoulli numbers are given.Comment: 43 pages. v.ii. Puzzle eliminated, references added and typos corrected. v.iii. topological arguments included, references adde

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

Outer membrane protein folding from an energy landscape perspective

The cell envelope is essential for the survival of Gram-negative bacteria. This specialised membrane is densely packed with outer membrane proteins (OMPs), which perform a variety of functions. How OMPs fold into this crowded environment remains an open question. Here, we review current knowledge about OFMP folding mechanisms in vitro and discuss how the need to fold to a stable native state has shaped their folding energy landscapes. We also highlight the role of chaperones and the β-barrel assembly machinery (BAM) in assisting OMP folding in vivo and discuss proposed mechanisms by which this fascinating machinery may catalyse OMP folding