Lawrence Livermore National Security

The NCEP–DOE Atmospheric Model Intercomparison Project (AMIP-II) reanalysis is a follow-on project to the “50-year” (1948–present) NCEP–NCAR Reanalysis Project. NCEP–DOE AMIP-II re-analysis covers the “20-year” satellite period of 1979 to the present and uses an updated forecast model, updated data assimilation system, improved diagnostic outputs, and fixes for the known processing problems of the NCEP–NCAR reanalysis. Only minor differences are found in the primary analysis variables such as free atmospheric geopotential height and winds in the Northern Hemisphere extratropics, while significant improvements upon NCEP–NCAR reanalysis are made in land surface parameters and land–ocean fluxes. This analysis can be used as a supplement to the NCEP–NCAR reanalysis especially where the original analysis has problems. The differences between the two analyses also provide a measure of uncertainty in current analyses.

Graphene is readily p-doped by adsorbates, but for device applications, it would be useful to access the n-doped material. Individual graphene nanoribbons were covalently functionalized by nitrogen species through high-power electrical joule heating in ammonia gas, leading to n-type electronic doping consistent with theory. The formation of the carbon-nitrogen bond should occur mostly at the edges of graphene where chemical reactivity is high. X-ray photoelectron spectroscopy and nanometer-scale secondary ion mass spectroscopy confirm the carbon-nitrogen species in graphene thermally annealed in ammonia. We fabricated an n-type graphene field-effect transistor that operates at room temperature.

Metal-organic frameworks (MOFs) are a class of hybrid materials with unique optical and electronic properties arising from rational self-assembly of the organic linkers and metal ions/clusters, yielding myriads of possible structural motifs. The combination of order and chemical tunability, coupled with good environmental stability of MOFs, are prompting many research groups to explore the possibility of incorporating these materials as active components in devices such as solar cells, photodetectors, radiation detectors, and chemical sensors. Although this field is only in its incipiency, many new fundamental insights relevant to integrating MOFs with such devices have already been gained. In this review, we focus our attention on the basic requirements and structural elements needed to fabricate MOF-based devices and summarize the current state of MOF research in the area of electronic, opto-electronic and sensor devices. We summarize various approaches to designing active MOFs, creation of hybrid material systems combining MOFs with other materials, and assembly and integration of MOFs with device hardware. Critical directions of future research are identified, with emphasis on achieving the desired MOF functionality in a device and establishing the structure-property relationships to identify and rationalize the factors that impact device performance.

Correction for 'An updated roadmap for the integration of metal-organic frameworks with electronic devices and chemical sensors' by Ivo Stassen et al., Chem. Soc. Rev., 2017, DOI: 10.1039/c7cs00122c.

We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed. LGA also allows the clustering of similar fragments of protein structures.

Soil is the largest terrestrial reservoir of organic carbon and is central for climate change mitigation and carbon-climate feedbacks. Chemical and physical associations of soil carbon with minerals play a critical role in carbon storage, but the amount and global capacity for storage in this form remain unquantified. Here, we produce spatially-resolved global estimates of mineral-associated organic carbon stocks and carbon-storage capacity by analyzing 1144 globally-distributed soil profiles. We show that current stocks total 899 Pg C to a depth of 1 m in non-permafrost mineral soils. Although this constitutes 66% and 70% of soil carbon in surface and deeper layers, respectively, it is only 42% and 21% of the mineralogical capacity. Regions under agricultural management and deeper soil layers show the largest undersaturation of mineral-associated carbon. Critically, the degree of undersaturation indicates sequestration efficiency over years to decades. We show that, across 103 carbon-accrual measurements spanning management interventions globally, soils furthest from their mineralogical capacity are more effective at accruing carbon; sequestration rates average 3-times higher in soils at one tenth of their capacity compared to soils at one half of their capacity. Our findings provide insights into the world's soils, their capacity to store carbon, and priority regions and actions for soil carbon management.

increase simulation) for the CMIP6 models of 1.7°C (1.3°C to 3.0°C) is only slightly larger than for the CMIP3 and CMIP5 models. Here we review and synthesize the latest developments in ECS and TCR values in CMIP, compile possible reasons for the current values as supplied by the modeling groups, and highlight future directions. Cloud feedbacks and cloud-aerosol interactions are the most likely contributors to the high values and increased range of ECS in CMIP6.

The KamLAND experiment has determined a precise value for the neutrino oscillation parameter $\ensuremath{\Delta}{m}_{21}^{2}$ and stringent constraints on ${\ensuremath{\theta}}_{12}$. The exposure to nuclear reactor antineutrinos is increased almost fourfold over previous results to $2.44\ifmmode\times\else\texttimes\fi{}{10}^{32}\text{ }\text{ }\mathrm{proton}\text{ }\mathrm{yr}$ due to longer livetime and an enlarged fiducial volume. An undistorted reactor ${\overline{\ensuremath{\nu}}}_{e}$ energy spectrum is now rejected at $>5\ensuremath{\sigma}$. Analysis of the reactor spectrum above the inverse beta decay energy threshold, and including geoneutrinos, gives a best fit at $\ensuremath{\Delta}{m}_{21}^{2}={7.58}_{\ensuremath{-}0.13}^{+0.14}(\mathrm{stat}{)}_{\ensuremath{-}0.15}^{+0.15}(\mathrm{syst})\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}\text{ }\text{ }{\mathrm{eV}}^{2}$ and ${tan}^{2}{\ensuremath{\theta}}_{12}={0.56}_{\ensuremath{-}0.07}^{+0.10}(\mathrm{stat}{)}_{\ensuremath{-}0.06}^{+0.10}(\mathrm{syst})$. Local $\ensuremath{\Delta}{\ensuremath{\chi}}^{2}$ minima at higher and lower $\ensuremath{\Delta}{m}_{21}^{2}$ are disfavored at $>4\ensuremath{\sigma}$. Combining with solar neutrino data, we obtain $\ensuremath{\Delta}{m}_{21}^{2}={7.59}_{\ensuremath{-}0.21}^{+0.21}\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}\text{ }\text{ }{\mathrm{eV}}^{2}$ and ${tan}^{2}{\ensuremath{\theta}}_{12}={0.47}_{\ensuremath{-}0.05}^{+0.06}$.

The protamines are a diverse family of small arginine-rich proteins that are synthesized in the late-stage spermatids of many animals and plants and bind to DNA, condensing the spermatid genome into a genetically inactive state. Vertebrates have from one to 15 protamine genes per haploid genome, which are clustered together on the same chromosome. Comparison of protamine gene and amino-acid sequences suggests that the family evolved from specialized histones through protamine-like proteins to the true protamines. Structural elements present in all true protamines are a series of arginine-rich DNA-anchoring domains (often containing a mixture of arginine and lysine residues in non-mammalian protamines) and multiple phosphorylation sites. The two protamines found in mammals, P1 and P2, are the most widely studied. P1 packages sperm DNA in all mammals, whereas protamine P2 is present only in the sperm of primates, many rodents and a subset of other placental mammals. P2, but not P1, is synthesized as a precursor that undergoes proteolytic processing after binding to DNA and also binds a zinc atom, the function of which is not known. P1 and P2 are phosphorylated soon after their synthesis, but after binding to DNA most of the phosphate groups are removed and cysteine residues are oxidized, forming disulfide bridges that link the protamines together. Both P1 and P2 have been shown to be required for normal sperm function in primates and many rodents.

We have developed detailed emission inventories for the amount of both black and organic carbon particles from biomass burning sources (wood fuel, charcoal burning, dung, charcoal production, agricultural, savanna and forest fires). We have also estimated an inventory for organic carbon particles from fossil fuel burning and urban activities from an existing inventory for fossil fuel sources of black carbon. We also provide an estimate for the natural source of organic matter. These emissions have been used together with our global aerosol model to study the global distribution of carbonaceous aerosols. The accuracy of the inventories and the model formulation has been tested by comparing the model simulations of carbonaceous aerosols in the atmosphere and in precipitation with observations reported in the literature. For most locations and seasons, the predicted concentrations are in reasonable agreement with the observations, although the model underpredicts black carbon concentrations in polar regions. The predicted concentrations in remote areas are extremely sensitive to both the rate of removal by wet deposition and the height of injection of the aerosols. Finally, a global map of the aerosol single scattering albedo was developed from the simulated carbonaceous particle distribution and a previously developed model for aerosol sulfates. The computed aerosol single scattering albedos compare well with observations, suggesting that most of the important aerosol species have been included in the model. For most locations and seasons, the single scattering albedo is larger than 0.85, indicating that these aerosols, in general, lead to a net cooling.

Laser powder bed fusion additive manufacturing is an emerging 3D printing technique for the fabrication of advanced metal components. Widespread adoption of it and similar additive technologies is hampered by poor understanding of laser-metal interactions under such extreme thermal regimes. Here, we elucidate the mechanism of pore formation and liquid-solid interface dynamics during typical laser powder bed fusion conditions using in situ X-ray imaging and multi-physics simulations. Pores are revealed to form during changes in laser scan velocity due to the rapid formation then collapse of deep keyhole depressions in the surface which traps inert shielding gas in the solidifying metal. We develop a universal mitigation strategy which eliminates this pore formation process and improves the geometric quality of melt tracks. Our results provide insight into the physics of laser-metal interaction and demonstrate the potential for science-based approaches to improve confidence in components produced by laser powder bed fusion.

UNLABELLED: We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved version of kSNP v2. AVAILABILITY AND IMPLEMENTATION: kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/ CONTACT: barryghall@gmail.com.

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

The National Ignition Facility (NIF) is the world's largest laser system. It contains a 192 beam neodymium glass laser that is designed to deliver 1.8 MJ at 500 TW at 351 nm in order to achieve energy gain (ignition) in a deuterium-tritium nuclear fusion target. To meet this goal, laser design criteria include the ability to generate pulses of up to 1.8 MJ total energy, with peak power of 500 TW and temporal pulse shapes spanning 2 orders of magnitude at the third harmonic (351 nm or 3omega) of the laser wavelength. The focal-spot fluence distribution of these pulses is carefully controlled, through a combination of special optics in the 1omega (1053 nm) portion of the laser (continuous phase plates), smoothing by spectral dispersion, and the overlapping of multiple beams with orthogonal polarization (polarization smoothing). We report performance qualification tests of the first eight beams of the NIF laser. Measurements are reported at both 1omega and 3omega, both with and without focal-spot conditioning. When scaled to full 192 beam operation, these results demonstrate, to the best of our knowledge for the first time, that the NIF will meet its laser performance design criteria, and that the NIF can simultaneously meet the temporal pulse shaping, focal-spot conditioning, and peak power requirements for two candidate indirect drive ignition designs.

Heterocyclic amines (HAs) are formed as pyrolysis products during the cooking of meats/fish. These substances are potent mutagens in the Ames/Salmonella assay and are also carcinogens in laboratory animals. In order to assess the magnitude of the cancer risk posed by their presence in the US diet, we estimated the average intakes of HAs, based on analyses of the concentrations of HAs in cooked foods and data from a dietary survey of the US population and quantified the cancer potencies of the individual compounds using dose-response data from animal bioassays. Measured concentrations of HAs in cooked foods were taken from a major review of the open literature. Only those concentrations that were associated with normal cooking conditions were chosen for use in estimating dietary intakes. The average consumption of HA-bearing foods was determined by analyzing statistically the intakes of 3563 individuals who provided 3 day dietary records in a USDA sponsored random survey of the US population during 1989. Dietary intakes of the five principal HAs in descending order were 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine (PhIP) > 2-amino-9H-pyrido[2,3-b]indole (A alpha C) > 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) > 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx) > 2-amino-3-methylimidazo[4,5-f]quinoline (IQ). The carcinogenic potencies, in contrast, were almost the reverse order: IQ > DiMeIQx > MeIQx > PhIP > A alpha C. An upper-bound estimate of the incremental cancer risk is 1.1 x 10(-4), using cancer potencies based on a body surface area basis. Nearly half (46%) of the incremental risk was due to ingestion of PhIP. Consumption of meat and fish products contributed the most (approximately 80%) to total risk.

Abstract Obtaining a burning plasma is a critical step towards self-sustaining fusion energy 1 . A burning plasma is one in which the fusion reactions themselves are the primary source of heating in the plasma, which is necessary to sustain and propagate the burn, enabling high energy gain. After decades of fusion research, here we achieve a burning-plasma state in the laboratory. These experiments were conducted at the US National Ignition Facility, a laser facility delivering up to 1.9 megajoules of energy in pulses with peak powers up to 500 terawatts. We use the lasers to generate X-rays in a radiation cavity to indirectly drive a fuel-containing capsule via the X-ray ablation pressure, which results in the implosion process compressing and heating the fuel via mechanical work. The burning-plasma state was created using a strategy to increase the spatial scale of the capsule 2,3 through two different implosion concepts 4–7 . These experiments show fusion self-heating in excess of the mechanical work injected into the implosions, satisfying several burning-plasma metrics 3,8 . Additionally, we describe a subset of experiments that appear to have crossed the static self-heating boundary, where fusion heating surpasses the energy losses from radiation and conduction. These results provide an opportunity to study α-particle-dominated plasmas and burning-plasma physics in the laboratory.

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.

The use of automated, unmanned aerial vehicles (drones) to deliver commercial packages is poised to become a new industry, significantly shifting energy use in the freight sector. Here we find the current practical range of multi-copters to be about 4 km with current battery technology, requiring a new network of urban warehouses or waystations as support. We show that, although drones consume less energy per package-km than delivery trucks, the additional warehouse energy required and the longer distances traveled by drones per package greatly increase the life-cycle impacts. Still, in most cases examined, the impacts of package delivery by small drone are lower than ground-based delivery. Results suggest that, if carefully deployed, drone-based delivery could reduce greenhouse gas emissions and energy use in the freight sector. To realize the environmental benefits of drone delivery, regulators and firms should focus on minimizing extra warehousing and limiting the size of drones.

The results of detailed experiments and finite element modeling of metal micro-droplet motion associated with metal additive manufacturing (AM) processes are presented. Ultra high speed imaging of melt pool dynamics reveals that the dominant mechanism leading to micro-droplet ejection in a laser powder bed fusion AM is not from laser induced recoil pressure as is widely believed and found in laser welding processes, but rather from vapor driven entrainment of micro-particles by an ambient gas flow. The physics of droplet ejection under strong evaporative flow is described using simulations of the laser powder bed interactions to elucidate the experimental results. Hydrodynamic drag analysis is used to augment the single phase flow model and explain the entrainment phenomenon for 316 L stainless steel and Ti-6Al-4V powder layers. The relevance of vapor driven entrainment of metal micro-particles to similar fluid dynamic studies in other fields of science will be discussed.