The precise measurement of time has been a goal of physicists for centuries. With every new increase in our ability to measure time we have discovered new phenomena. The most advanced clocks available to us currently are atomic clocks that use electronic transitions to track the passage of time. In this proposal, I put forward the framework for the first nuclear clock estimated to be 1000 to 10000 times more precise than the current atomic clocks. This research will explore in detail the atomic nuclear interactions and help perfect and refine current atomic-nuclear interaction models. The realization of a {sup 229}Th nuclear clock will allow tests of cosmology by measuring the change of the fine structure constant as a function of time. The results of these experiments could dramatically alter our view of the universe, its past and future evolution. Precision clocks - with fundamental physics applications - require a long-lived quantum transition (two-level system) that is immune to external perturbations. Nuclear transitions would be better suited than atomic transitions for these applications except that nuclear transitions are typically much higher in energy and therefore cannot be accessed with table-top lasers. There is, however, one promising nuclear transition: the doublet …

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 …

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 …

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 …

Over the last several years increasing energy and petroleum prices have propelled biofuels and the feedstocks used to produce them, to the forefront of alternative energy production. This growth has increased the linkages between energy and agricultural markets and these changes around the world are having a significant effect on agricultural markets as biofuels begin to play a more substantial role in meeting the world's energy needs. Biofuels are alternatively seen as a means to reduce carbon emissions, increase energy independence, support rural development and to raise farm income. However, concern has arisen that the new demand for traditional commodities or alternative commodities which compete for land can lead to higher food prices and the environmental effects from expanding crop acreage may result in uncertain changes in carbon emissions as land is converted both in the US and abroad. While a number of studies examine changes in land use and consumption from changes in biofuels policies many lack effective policy representation or complete coverage of land types which may be diverted in to energy feedstock production. Many of these biofuels and renewable energy induced land use changes are likely to occur in developing countries with at-risk consumers and on environmentally …

In this paper, we propose a novel mesh coarsening method called brick coarsening method. The proposed method can be used in conjunction with any graph partitioners and scales to very large meshes. This method reduces problem space by decomposing the original mesh into fixed-size blocks of nodes called bricks, layered in a similar way to conventional brick laying, and then assigning each node of the original mesh to appropriate brick. Our experiments indicate that the proposed method scales to very large meshes while allowing simple RCB partitioner to produce higher-quality partitions with significantly less edge cuts. Our results further indicate that the proposed brick-coarsening method allows more complicated partitioners like PT-Scotch to scale to very large problem size while still maintaining good partitioning performance with relatively good edge-cut metric. Graph partitioning is an important problem that has many scientific and engineering applications in such areas as VLSI design, scientific computing, and resource management. Given a graph G = (V,E), where V is the set of vertices and E is the set of edges, (k-way) graph partitioning problem is to partition the vertices of the graph (V) into k disjoint groups such that each group contains roughly equal number of vertices …

An experts' workshop was convened in Dublin Ireland September 27th – 28th 2010 in support of IEA Ocean Energy Systems Implementing Agreement Annex IV. PNNL was responsible for organizing the content of the workshop, overseeing the contractors (Irish Marine Institute) hosting the event, presenting material on Annex IV and materials applicable to the workshop intent. PNNL is also overseeing a contractor (Wave Energy Center/University of Plymouth – WEC/UP) in the collection and analysis of the Annex IV data. Fifty-eight experts from 8 countries attended the workshop by invitation, spending two days discussing the needs of Annex IV. Presentations by DOE (background on Annex IV), PNNL (process for developing Annex IV; presentation of the draft database for PNNL project, plans for incorporating Annex IV data), WEC/UP on the environmental effect matrix, and four MHK developers (two from the UK, one from Ireland and one from Sweden; each discussing their own projects and lessons learned for measuring and mitigating environmental effects, as well as interactions with consenting [permitting] processes) helped provide background. The workshop participants worked part of the time in the large group and most of the time in four smaller breakout groups. Participants engaged in the process and provided 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.

Airborne electromagnetic (AEM) surveys were flown during fiscal year (FY) 2008 within the 600 Area in an attempt to characterize the underlying subsurface and to aid in the closure and remediation design study goals for the 200-PO-1 Groundwater Operable Unit (OU). The rationale for using the AEM surveys was that airborne surveys can cover large areas rapidly at relatively low costs with minimal cultural impact, and observed geo-electrical anomalies could be correlated with important subsurface geologic and hydrogeologic features. Initial interpretation of the AEM surveys indicated a tenuous correlation with the underlying geology, from which several anomalous zones likely associated with channels/erosional features incised into the Ringold units were identified near the River Corridor. Preliminary modeling resulted in a slightly improved correlation but revealed that more information was required to constrain the modeling (SGW-39674, Airborne Electromagnetic Survey Report, 200-PO-1 Groundwater Operable Unit, 600 Area, Hanford Site). Both time-and frequency domain AEM surveys were collected with the densest coverage occurring adjacent to the Columbia River Corridor. Time domain surveys targeted deeper subsurface features (e.g., top-of-basalt) and were acquired using the HeliGEOTEM{reg_sign} system along north-south flight lines with a nominal 400 m (1,312 ft) spacing. The frequency domain RESOLVE system acquired electromagnetic …

For decades, computer scientists have sought guidance on how to evolve architectures, languages, and programming models in order to improve application performance, efficiency, and productivity. Unfortunately, without overarching advice about future directions in these areas, individual guidance is inferred from the existing software/hardware ecosystem, and each discipline often conducts their research independently assuming all other technologies remain fixed. In today's rapidly evolving world of on-chip parallelism, isolated and iterative improvements to performance may miss superior solutions in the same way gradient descent optimization techniques may get stuck in local minima. To combat this, we present TORCH: A Testbed for Optimization ResearCH. These computational reference kernels define the core problems of interest in scientific computing without mandating a specific language, algorithm, programming model, or implementation. To compliment the kernel (problem) definitions, we provide a set of algorithmically-expressed verification tests that can be used to verify a hardware/software co-designed solution produces an acceptable answer. Finally, to provide some illumination as to how researchers have implemented solutions to these problems in the past, we provide a set of reference implementations in C and MATLAB.