We demonstrate a technique to nanofabricate nitrogen vacancy (NV) centers in diamond based on broad-beam nitrogen implantation through apertures in electron beam lithography resist. This method enables high-throughput nanofabrication of single NV centers on sub-100-nm length scales. Secondary ion mass spectroscopy measurements facilitate depth profiling of the implanted nitrogen to provide three-dimensional characterization of the NV center spatial distribution. Measurements of NV center coherence with on-chip coplanar waveguides suggest a pathway for incorporating this scalable nanofabrication technique in future quantum applications.

Human biospecimens are subjected to collection, processing, and storage that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research that uses human tissues, it is crucial that information on the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications on biospecimen-related research and to help reassure patient contributors and the advocacy community that their contributions are valued and respected.

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected 'burning' regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions.

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Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a …

Silo and HDF5 are I/O libraries used by many codes important to the LLNL's Weapons and Complex Integration (WCI) mission. In the past year, modest adjustments and tuning of Silo, HDF5 and the I/O configuration of the BG/P platform, Dawn, were undertaken. A key goal of this work was to improve I/O performance without requiring any changes in the application codes themselves. In particular, the application codes have been allowed to continue to use a simplified yet highly flexible I/O paradigm known as 'Poor Man's Parallel I/O', where scalability is achieved through concurrent, serial I/O to multiple files. The results demonstrate substantial performance gains (better than 50x in many cases) at large scale (greater than 64,000 MPI tasks). They describe key enhancements made to Silo, HDF5 and the I/O configuration of our BG/P platform and present very favorable results from scalability studies over a wide range of operating scenarios.

The 2010 Gordon Research Conference on Polymer Physics will provide outstanding lectures and discussions in this critical field that impacts every industrial sector from electronics to transportation to medicine to textiles to energy generation and storage. Fundamental topics range from mechanical properties of soft gels to new understanding in polymer crystallization to energy conversion and transmission to simulating polymer dynamics at the nanoscale. This international conference will feature 22 invited lectures, wherein the opening 10 minutes are specifically designed for a general polymer physics audience. In addition, poster sessions and informal activities provide ample opportunity to discuss the latest advances in polymer physics. The technical content of the meeting will include new twists on traditional polymer physics topics, recent advances in previously underrepresented topics, and emerging technologies enabled by polymer physics. Here is a partially listing of targeted topics: (1) electrically-active and light-responsive polymers and polymer-based materials used in energy conversion and storage; (2) polymers with hierarchical structures including supramolecular assemblies, ion-containing polymers, and self-assembled block polymers; (3) mechanical and rheological properties of soft materials, such as hydrogels, and of heterogeneous materials, particularly microphase separated polymers and polymer nanocomposites; and (4) crystallization of polymers in dilute solutions, polymer melts, and …

The National Ignition Facility (NIF) is the largest and most energetic laser in the world contained in a complex the size of a football stadium. From the initial laser pulse, provided by telecommunication style infrared nanoJoule pulsed lasers, to the final 192 laser beams (1.8 Mega Joules total energy in the ultraviolet) converging on a target the size of a pencil eraser, laser safety is of paramount concern. In addition to this, there are numerous high-powered (Class 3B and 4) diagnostic lasers in use that can potentially send their laser radiation travelling throughout the facility. With individual beam paths of up to 1500 meters and a workforce of more than one thousand, the potential for exposure is significant. Simple laser safety practices utilized in typical laser labs just don't apply. To mitigate these hazards, NIF incorporates a multi layered approach to laser safety or 'Defense in Depth.' Most typical high-powered laser operations are contained and controlled within a single room using relatively simplistic controls to protect both the worker and the public. Laser workers are trained, use a standard operating procedure, and are required to wear Personal Protective Equipment (PPE) such as Laser Protective Eyewear (LPE) if the system is …

The Final Optics Damage Inspection (FODI) system automatically acquires and utilizes the Optics Inspection (OI) system to analyze images of the final optics at the National Ignition Facility (NIF). During each inspection cycle up to 1000 images acquired by FODI are examined by OI to identify and track damage sites on the optics. The process of tracking growing damage sites on the surface of an optic can be made more effective by identifying and removing signals associated with debris or reflections. The manual process to filter these false sites is daunting and time consuming. In this paper we discuss the use of machine learning tools and data mining techniques to help with this task. We describe the process to prepare a data set that can be used for training and identifying hardware reflections in the image data. In order to collect training data, the images are first automatically acquired and analyzed with existing software and then relevant features such as spatial, physical and luminosity measures are extracted for each site. A subset of these sites is 'truthed' or manually assigned a class to create training data. A supervised classification algorithm is used to test if the features can predict the …

A relatively new technique for measuring the electron cloud density in storage rings has been developed and successfully demonstrated [S. De Santis, J.M. Byrd, F. Caspers, A. Krasnykh, T. Kroyer, M.T.F. Pivi, and K.G. Sonnad, Phys. Rev. Lett. 100, 094801 (2008).]. We present the experimental results of a systematic application of this technique at the Cornell Electron Storage Ring Test Accelerator. The technique is based on the phase modulation of the TE mode transmitted in a synchrotron beam pipe caused by the periodic variation of the density of electron plasma. Because of the relatively simple hardware requirements, this method has become increasingly popular and has been since successfully implemented in several machines. While the principles of this technique are straightforward, quantitative derivation of the electron cloud density from the measurement requires consideration of several effects, which we address in detail.

Catalysis is a key technology for improving the quality of life while simultaneously reducing the adverse impact of human activities on the environment. The discovery of new catalytic processes and the improvement of existing ones are also critically important for securing the nation's energy supply. The GRC on Catalysis is considered one the most prestigious conference for catalysis research, bringing together leading researchers from both academia, industry and national labs to discuss the latest, most exciting research in catalysis and the future directions for the field. The 2010 GRC on Catalysis will follow time-honored traditions and feature invited talks from the world's leading experts in the fundamentals and applications of catalytic science and technology. We plan to have increased participation from industry. The extended discussions in the company of outstanding thinkers will stimulate and foster new science. The conference will include talks in the following areas: Alternative feedstocks for chemicals and fuels, Imaging and spectroscopy, Design of novel catalysts, Catalyst preparation fundamentals, Molecular insights through theory, Surface Science, Catalyst stability and dynamics. In 2010, the Catalysis conference will move to a larger conference room with a new poster session area that will allow 40 posters per session. The dorm rooms …

A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.

New scientific applications require phase-stabilized RF distribution to multiple remote locations. These include phased-array radio telescopes and short pulse free electron lasers. RF modulated onto a CW optical carrier and transmitted via fiber is capable of low noise, but commercially available systems aren't long term stable enough for these applications. Typical requirements are for less than 50fs long term temporal stability between receivers, which is 0.05 degrees at 3GHz. Good results have been demonstrated for RF distribution schemes based on transmission of short pulses, but these require specialized free-space optics and high stability mechanical infrastructure. We report a method which uses only standard telecom optical and RF components, and achieves less than 20fs RMS error over 300m of standard single-mode fiber. We demonstrate stable transmission of 3GHz over 300m of fiber with less than 0.017 degree (17fs) RMS phase error. An interferometer measures optical phase delay, providing information to a feed-forward correction of RF phase.

The ability of a cell to distribute contractile stresses across the extracellular matrix in a spatially heterogeneous fashion underlies many cellular behaviors, including motility and tissue assembly. Here we investigate the biophysical basis of this phenomenon by using femtosecond laser nanosurgery to measure the viscoelastic recoil and cell-shape contributions of contractile stress fibers (SFs) located in specific compartments of living cells. Upon photodisruption and recoil, myosin light chain kinase-dependent SFs located along the cell periphery display much lower effective elasticities and higher plateau retraction distances than Rho-associated kinase-dependent SFs located in the cell center, with severing of peripheral fibers uniquely triggering a dramatic contraction of the entire cell within minutes of fiber irradiation. Image correlation spectroscopy reveals that when one population of SFs is pharmacologically dissipated, actin density flows toward the other population. Furthermore, dissipation of peripheral fibers reduces the elasticity and increases the plateau retraction distance of central fibers, and severing central fibers under these conditions triggers cellular contraction. Together, these findings show that SFs regulated by different myosin activators exhibit different mechanical properties and cell shape contributions. They also suggest that some fibers can absorb components and assume mechanical roles of other fibers to stabilize cell shape.

The emergence of enhanced spontaneous magnetic moments in self-assembled, epitaxial nanostructures of tetragonal (T-phase) and rhombohedral phases (R-phase) of the multiferroic BiFeO{sub 3} system is demonstrated. X-ray magnetic circular dichroism based photoemission electron microscopy (PEEM) was applied to investigate the local nature of this magnetism. We find that the spontaneous magnetization of the R-phase is significantly enhanced above the canted antiferromagnetic moment in the bulk phase, as a consequence of a piezomagnetic coupling to the adjacent T-phase and the epitaxial constraint. Reversible electric field control and manipulation of this magnetic moment at room temperature is shown using a combination of piezoresponse force microscopy and PEEM studies.

Using a novel, phase-stabilized RF-over-fiber scheme, they transmit 3GHz over 300m with 27fs RMS error in 250kHz bandwidth over 12 hours, and phase lock a laser to enable ultrafast pump-probe experiments. Free-electron lasers (FELs) are capable of producing short-duration (< 10fs), high-energy X-ray pulses for a range of scientific applications. The recently activated Linac Coherent Light Source (LCLS) FEL facility at SLAC will support experiments which require synchronized light pulses for pump-probe schemes. They developed and operated a fiber optic RF transmission system to synchronize lasers to the emitted X-ray pulses, which was used to enable the first pump-probe experiments at the LCLS.

We investigate tunable plasmon resonant cavity arrays in paired parallel nanowire waveguides. Resonances are observed when the waveguide length is an odd multiple of quarter plasmon wavelengths, consistent with boundary conditions of node and antinode at the ends. Two nanowire waveguides satisfy the dispersion relation of a planar metal-dielectric-metal waveguide of equivalent width equal to the square field average weighted gap. Confinement factors over 10{sup 3} are possible due to plasmon focusing in the inter-wire space.

A mechanism for creating and selecting amino acid chirality is identified, and subsequent chemical replication and galactic mixing that would populate the galaxy with the predominant species will be described. This involves: (1) the spin of the {sup 14}N in the amino acids, or in precursor molecules from which amino acids might be formed, coupling to the chirality of the molecules; (2) the neutrinos emitted from the supernova, together with magnetic field from the nascent neutron star or black hole from the supernova selectively destroying one orientation of the {sup 14}N, thereby selecting the chirality associated with the other {sup 14}N orientation; (3) amplification by chemical evolution, by which the molecules replicate on a relatively short timescale; and (4) galactic mixing on a longer timescale mixing the selected molecules throughout the galaxy.

Historical records from the Department of Energy Hanford Nuclear Reservation (in eastern WA) indicate that ruptures in buried waste transfer pipelines were common between the 1940s and 1980s, which resulted in unplanned releases (UPRs) of tank: waste at numerous locations. A number of methods are commercially available for the detection of active or recent leaks, however, there are no methods available for the detection of leaks that occurred many years ago. Over the decades, leaks from the Hanford pipelines were detected by visual observation of fluid on the surface, mass balance calculations (where flow volumes were monitored), and incidental encounters with waste during excavation or drilling. Since these detection methods for historic leaks are so limited in resolution and effectiveness, it is likely that a significant number of pipeline leaks have not been detected. Therefore, a technology was needed to detect the specific location of unknown pipeline leaks so that characterization technologies can be used to identify any risks to groundwater caused by waste released into the vadose zone. A proof-of-concept electromagnetic geophysical survey was conducted at an UPR in order to image a historical leak from a waste transfer pipeline. The survey was designed to test an innovative electromagnetic …

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Hydrogen and oxygen generation due to the radiolysis of water is a recognized hazard in pipe systems used in the nuclear industry, where the accumulation of hydrogen and oxygen at high points in the pipe system is expected, and explosive conditions exist. Pipe ruptures at nuclear facilities were attributed to hydrogen explosions inside pipelines, in nuclear facilities, i.e., Hamaoka, Nuclear Power Station in Japan, and Brunsbuettel in Germany. Prior to these accidents an ignition source for hydrogen was questionable, but these accidents, demonstrated that a mechanism was, in fact, available to initiate combustion and explosion. Hydrogen explosions may occur simultaneously with water hammer accidents in nuclear facilities, and a theoretical mechanism to relate water hammer to hydrogen deflagrations and explosions is presented herein.