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At least 1,261 records · Page 70

In-Field Whole-Plant Maize Architecture Characterized by Subcanopy Rovers and Latent Space Phenotyping

Core Ideas * Subcanopy rovers enabled 3D characterization of thousands of hybrid maize plots. * Machine learning produces heritable latent traits that describe plant architecture. * Rover-based phenotyping is far more efficient than manual phenotyping. * Latent phenotypes from rovers are ready for application to plant biology and breeding. Collecting useful, interpretable, and biologically relevant phenotypes in a resource-efficient manner is a bottleneck to plant breeding, genetic mapping, and genomic prediction. Autonomous and affordable subcanopy rovers are an efficient and scalable way to generate sensor-based datasets of in-field crop plants. Rovers equipped with lidar can produce three-dimensional reconstructions of entire hybrid maize (Zea mays L.) fields. In this study, we collected 2103 lidar scans of hybrid maize field plots and extracted phenotypic data from them by latent space phenotyping. We performed latent space phenotyping by two methods, principal component analysis and a convolutional autoencoder, to extract meaningful, quantitative latent space phenotypes (LSPs) describing whole-plant architecture and biomass distribution. The LSPs had heritabilities of up to 0.44, similar to some manually measured traits, indicating that they can be selected on or genetically mapped. Manually measured traits can be successfully predicted by using LSPs as explanatory variables in partial least squares regression, indicating that the LSPs contain biologically relevant information about plant architecture. These techniques can be used to assess crop architecture at a reduced cost and in an automated fashion for breeding, research, or extension purposes, as well as to create or inform crop growth models.

59 BASIC BIOLOGICAL SCIENCES↗

Rapidly rotating flow with weak stratification [Slides]

Theoretically as the rotation rate goes to infinity (Ro->0 here) the 'slow' component of the flow determines the full evolution of the system. Here we decompose the full solution into 'slow' S and fluctuating ' components. The left plot below is the full horizontal kinetic energy (upper, dashed lines) and 'slow' horizontal kinetic energy (lower solid lines). Note that the difference appears to be constant for all time. The right plot below is the exchange of energy from the fluctuations to the 'slow' component. Note that it has a definite sign, meaning all the fluctuating energy is converted to 'slow'.

58 GEOSCIENCES↗

EMPIRE-3.2 Malta: modular system for nuclear reaction calculations and nuclear data evaluation [User's Manual]

EMPIRE is a modular system of nuclear reaction codes, comprising various nuclear models, and designed for calculations over a broad range of energies and incident particles. The system can be used for theoretical investigations of nuclear reactions as well as for nuclear data evaluation work. Photons, nucleons, deuterons, tritons, helions (3He), α’s, and light or heavy ions can be selected as projectiles. The energy range starts just above the resonance region in the case of a neutron projectile, and extends up to few hundred MeV for heavy ion induced reactions. The code accounts for the major nuclear reaction models, such as optical model, Coupled Channels and DWBA (ECIS06 and OPTMAN), Multi-step Direct (ORION + TRISTAN), NVWY Multi-step Compound, exciton model (PCROSS), hybrid Monte Carlo simulation (DDHMS), and the full featured Hauser-Feshbach model including width fluctuations and the optical model for fission. Heavy ion fusion cross section can be calculated within the simplified coupled channels approach (CCFUS). A comprehensive library of input parameters based on the RIPL-3 library covers nuclear masses, optical model parameters, ground state deformations, discrete levels and decay schemes, level densities, fission barriers, and γ-ray strength functions. Effects of the dynamic deformation of a fast rotating nucleus can be taken into account in the calculations (BARFIT, MOMFIT). The results can be converted into the ENDF-6 format using the accompanying EMPEND code. Modules of the ENDF Utility Codes and the ENDF Pre-Processing codes are applied for ENDF file verification. The package contains the full EXFOR library of experimental data in computational format C4 that are automatically retrieved during the calculations. EMPIRE contains the resonance module that retrieves data from the electronic version of the Atlas of Neutron Resonances by Mughabghab (not provided with the EMPIRE distribution), to produce resonance section and related covariances for the ENDF-6 formatted files. EMPIRE can be used to determine covariances of the calculated data using either sensitivity matrices along with the KALMAN code or employing Monte Carlo approach to produce model generated covariances. In both cases experimental data can be taken into account, either directly (KALMAN) or by feeding the EMPIRE calculated Monte Carlo modelling covariance as a prior to the least square fitting GANDR system. Publication quality graphs can be obtained using the powerful and flexible plotting package ZVView. Interactive plots with ZVView comparing experimental results with calculations can be produced with ENDVER modules. The backbone of the EMPIRE system are bash-shell UNIX scripts that provide for seamless console operation of EMPIRE on Linux, Mac OS X, and Microsoft Windows with GNU gfortran compiler installed. Additionally, the graphical interface, provides for an easy operation of the system on Linux, Mac OS X and virtual Linux machines running on Microsoft Windows.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Meteorological services annual data report for 2012

This document presents the meteorological data collected at Brookhaven National Laboratory (BNL) by Meteorological Services (Met Services) for the calendar year 2012. The purpose is to publicize the data sets available to emergency personnel, researchers and facility operations. Met services has been collecting data at BNL since 1949. Data from 1994 to the present is available in digital format. Data is presented in monthly plots of one-minute data. This allows the reader the ability to peruse the data for trends or anomalies that may be of interest to them. Full data sets are available to BNL personnel and to a limited degree outside researchers. The full data sets allow plotting the data on expanded time scales to obtain greater details (e.g., daily solar variability, inversions, etc.).

54 ENVIRONMENTAL SCIENCES↗

Meteorological Services: Annual Data Report for 2013

This document presents the meteorological data collected at Brookhaven National Laboratory (BNL) by Meteorological Services (Met Services) for the calendar year 2013. The purpose is to publicize the data sets available to emergency personnel, researchers and facility operations. Met services has been collecting data at BNL since 1949. Data from 1994 to the present is available in digital format. Data is presented in monthly plots of one-minute data. This allows the reader the ability to peruse the data for trends or anomalies that may be of interest to them. Full data sets are available to BNL personnel and to a limited degree outside researchers based on the level of time and resources required. The full data sets allow plotting the data on expanded time scales to obtain greater details (e.g., daily solar variability, inversions, etc.).

54 ENVIRONMENTAL SCIENCES↗

Climate Effects on Plant Range Distributions and Community Structure of Pacific Northwest Prairies

Pacific Northwest (PNW) prairies are an imperiled ecosystem that contain a large number of plant species with high fidelity to this habitat. The few remaining high-quality PNW prairies harbor a number of sensitive, rare, and endangered plant species that may be further at-risk with climate change. Thus, PNW prairies are an excellent model system to examine how climate change will affect the distribution of native plant species in grassland sites. Our experimental objectives were to determine: (i) how climate change will affect the range distribution of native plant species; (ii) what life history stages are most sensitive to climate change in a group of key indicator native species; (iii) the robustness of current restoration techniques and suites of species to changing climate, and in particular, the relative competitiveness of native species versus exotic invasive species; and (iv) the effects of climate change on carbon and nutrient cycling and soil-microbial-plant feedbacks. We addressed these objectives by experimentally increasing temperature 2.5 to 3.0 ºC above ambient with overhead infrared lamps and increasing wet-season precipitation by 20% above ambient in three upland prairie sites in central-western Washington, central-western Oregon, and southwestern Oregon from fall 2010 through 2012. Additional precipitation was applied within 2 weeks of when it fell so precipitation intensity was increased, particularly during the winter rainy season but with minimal additions during the summer dry season. These three sites also represent a 520-km natural climate gradient of increasing degree of severity of Mediterranean climate from north to south. After removing the extant vegetation, we planted a diverse suite of 12 native species that have their northern range limit someplace within the PNW in each experimental plot. An additional 20 more wide-spread native species were also planted into each plot. We found that recruitment of plant species within their ranges was negatively impacted by increased temperatures, but for species planted north of their current range, increased temperature was neutral. However, for surviving plants climate treatments and site-specific factors (e.g., nutrient availability) were the strongest predictors of plant growth and seed set. When recruitment and plant growth are considered together, increased temperatures are negative within a species current range but beyond this range they become positive. Germination was the most critical stage for plant response across all sites and climate treatments. Our results underscore the importance of including plant vital rates into models that are examining climate change effects on plant ranges. Warming altered plant community composition, decreased diversity, and increased total cover, with warmed northern communities over time becoming more like ambient communities further south. In particular, warming increased the cover of annual introduced species, suggesting that the observed biogeographic pattern of increasing invasion by this plant functional group in US West Coast prairies as one moves further south is at least in part due to climate. Our results suggest that with the projected increase in drought severity with climate change, Pacific Northwest prairies may face an increase of invasion by annuals, similar to what has been observed in California, resulting in novel species assemblages and shifts in functional composition, which in turn may alter ecosystem function. Warming generally increased nutrient availability and plant productivity across all sites. The seasonality of soil respiration responses to heating were strongly dependent on the Mediterranean climate gradient in the PNW, with heating responses being generally positive during periods of adequate soil moisture and becoming neutral to negative during periods of low soil moisture. The asynchrony between temperature and precipitation may make soils less sensitive to warming. Precipitation effects were minimal for all measured responses indicating the importance of increased temperatures in driving biotic responses to climate change in Mediterranean ecosystems. However, substantially increased precipitation during the dry season would almost certainly have profound effects, but the opposite is predicted by current climate change models for the PNW. A manipulative climate change experiment embedded within a natural climate gradient provides unique insights into the degree to which biotic responses to climate change are regionally consistent and site-dependent. Perhaps surprisingly, most climatic effects that we observed were either consistent in the three sites or could be readily interpreted in terms of the gradient of increasing intensity of the Mediterranean climate from north to south.

54 ENVIRONMENTAL SCIENCES↗

Guide to Using the WIND Toolkit Validation Code

In response to the U.S. Department of Energy's goal of using 20% wind energy by 2030, the Wind Integration National Dataset (WIND) Toolkit was created to provide information on wind speed, wind direction, temperature, surface air pressure, and air density on more than 126,000 locations across the United States from 2007 to 2013. The numerical weather prediction model output, gridded at 2-km and at a 5-minute resolution, was further converted to detail the wind power production time series of existing and potential wind facility sites. For users of the dataset it is important that the information presented in the WIND Toolkit is accurate and that errors are known, as then corrective steps can be taken. Therefore, we provide validation code written in R that will be made public to provide users with tools to validate data of their own locations. Validation is based on statistical analyses of wind speed, using error metrics such as bias, root-mean-square error, centered root-mean-square error, mean absolute error, and percent error. Plots of diurnal cycles, annual cycles, wind roses, histograms of wind speed, and quantile-quantile plots are created to visualize how well observational data compares to model data. Ideally, validation will confirm beneficial locations to utilize wind energy and encourage regional wind integration studies using the WIND Toolkit.

17 WIND ENERGY↗

Two-Dimensional Correlation Method for Polymer Analysis

Since its introduction by Noda in 1986 two-dimension correlation spectroscopy has been offering polymer scientists an opportunity to look more deeply into collected spectroscopic data. When the spectra are recorded in response to an external perturbation, it is possible to correlate the spectra and expand the information over a separate spectra axis allow for enhancement of spectral resolution, the ability to determine synchronous change, and a unique way to organize observed changes in the spectra into sequential order following a set of three simple rules. By organizing the 2D spectra into synchronous change plots and asynchronous change plots it is possible to correlate change between spectral regions and develop their temporal relationships to one another. With the introduction of moving-window correlation-spectroscopy by Thomas and Richardson in 2000, a method of binning and processing data, it became possible to directly correlate relationships generated in the spectra from the change in the perturbation variable. This method takes advantage of the added resolution of two-dimension spectroscopy and has been applied to study very week transitions found in polymer materials. Appling both of these techniques we are beginning to develop an understanding of how polymers decay under radiolytic aging, to develop a stronger understanding of changes in mechanical properties and the service capabilities of materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Meteorological Services Annual Data Report for 2014

This document presents the meteorological data collected at Brookhaven National Laboratory (BNL) by Meteorological Services (Met Services) for the calendar year 2014. The purpose is to publicize the data sets available to emergency personnel, researchers and facility operations. Met services has been collecting data at BNL since 1949. Data from 1994 to the present is available in digital format. Data is presented in monthly plots of one-minute data. This allows the reader the ability to peruse the data for trends or anomalies that may be of interest to them. Full data sets are available to BNL personnel and to a limited degree outside researchers. The full data sets allow plotting the data on expanded time scales to obtain greater details (e.g., daily solar variability, inversions, etc.).

54 ENVIRONMENTAL SCIENCES↗

Development of High Yield Feedstocks and Biomass Conversion Technology for Renewable Energy

This project had two main goals. The first goal was to evaluate several high yielding tropical perennial grasses as feedstock for biofuel production, and to characterize the feedstock for compatible biofuel production systems. The second goal was to assess the integration of renewable energy systems for Hawaii. The project focused on high-yield grasses (napiergrass, energycane, sweet sorghum, and sugarcane). Field plots were established to evaluate the effects of elevation (30, 300 and 900 meters above sea level) and irrigation (50%, 75% and 100% of sugarcane plantation practice) on energy crop yields and input. The test plots were extensive monitored including: hydrologic studies to measure crop water use and losses through seepage and evapotranspiration; changes in soil carbon stock; greenhouse gas flux (CO 2 , CH 4 , and N 2 O) from the soil surface; and root morphology, biomass, and turnover. Results showed significant effects of environment on crop yields. In general, crop yields decrease as the elevation increased, being more pronounced for sweet sorghum and energycane than napiergrass. Also energy crop yields were higher with increased irrigation levels, being most pronounced with energycane and less so with sweet sorghum. Daylight length greatly affected sweet sorghum growth and yields. One of the energy crops (napiergrass) was harvested at different ages (2, 4, 6, and 8 months) to assess the changes in feedstock characteristics with age and potential to generate co-products. Although there was greater potential for co-products from younger feedstock, the increased production was not sufficient to offset the additional cost of harvesting multiple times per year. The feedstocks were also characterized to assess their compatibility with biochemical and thermochemical conversion processes. The project objectives are being continued through additional support from the Office of Naval Research, and the Biomass Research and Development Initiative. Renewable energy assessments included: biomass feedstocks currently being produced by Hawaiian Commercial & Sugar Co., and possibilities of producing methane from agricultural and livestock wastes and the potential of photovoltaic systems for irrigation pumping at HC&S. Finally, the impact of a micro-hydroelectric system on a small-farm economics and the local community was assessed.

09 BIOMASS FUELS↗

Disk Mechanical Test Development

The target disks are held in a circular slot in a stainless steel holder. The holder is sized and toleranced so that the disks fit without constraint in the holder at the temperature of the parts under the irradiation condition. The target is a stack of 29 mm diameter disks 0.5 mm thick separated by 0.25 mm coolant gaps. The hottest disks reach a temperature of 1263 K at the center. Figure 1 shows the temperature contour plot of the hottest disk, Disk 14. Temperature increase causes thermal expansion through the thickness and radially. The radial thermal expansion in particular causes thermal stresses, aggravated by the fact that the center heats significantly more than the edge. Thus the center of the disk expands radially but the relatively cool outer edge constrains that motion. The resulting thermal stress is shown in Figure 2, showing a peak thermal stress of 281 MPa at the center. Stress/strain curves for molybdenum are shown in the plot in Figure 3. From the curve at 982°C, it is evident that plastic deformation will result, with a maximum deformation of 0.002 in (0.05 mm). Actual deformation is shown in Figures 4 and 5 in one radial plane and in the "Z" direction through the thickness.

36 MATERIALS SCIENCE↗

Forensic Analysis of Terrorist Counter-Financing to Combat Nuclear Proliferation

The single greatest threat to U.S. homeland security remains the proliferation of nuclear weapons, especially among terrorists and other non-state actors who are not governed by the Non-Proliferation Treaty. One of the most important tools for combating terrorism among such rogue actors is counter-financing. Without funding, terrorists cannot acquire, maintain, or deploy nuclear weapons. According to the official report of the 9/11 Commission, counter-financing could have prevented the attacks of September 11, 2001. Unfortunately, no single country can defeat global terrorism. Successful counter-financing requires significant international cooperation. Since 2001, the United States and the European Union, despite vastly different approaches to intelligence gathering, have shared information through the Terrorist Finance Tracking Program (TFTP). That shared information allows authorities to trace suspicious transactions, identify culprits, and map out global terrorist networks. The TFTP successfully thwarted a 2011 plot to assassinate the Saudi Arabian Ambassador to the U.S. and multiple threats during the 2012 Summer Olympics in London; it also aided in the investigation of the 2013 Boston Marathon bombing. That program is necessary but not sufficient. To strengthen our ability to detect and disrupt terrorist plotting and prevent nuclear proliferation, we must expand and coordinate two additional transnational measures: (1) the Society for Worldwide Interbank Financial Telecommunications (SWIFT), a standardized global messaging network for financial institutions to quickly, accurately, and securely send and receive money transfer instructions, and (2) International Bank Account Numbers (IBAN) to identify individual accounts involved in international transactions. Both initiatives were incompletely adopted in the wake of 9/11, but most global banks use one or neither. More fully implementing and coordinating these two systems would allow for coherent information sharing, an essential tool for combating money laundering and terrorist financing, verifying sanctions against rogue nations and non-state actors, tracking nuclear proliferation networks, and protecting dual-use materials. These steps can save lives without interfering with state sovereignty or individual rights. The specter of nuclear threat is real and constant. This paper will provide forensic analysis of the most effective financial tools and policies to combat that threat, placing special emphasis on multinational and public-private cooperation.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Uncertainty quantification tools for multiphase gas-solid flow simulations using MFIX

Computational fluid dynamics (CFD) has been widely studied and used in the scientific community and in the industry. Various models were proposed to solve problems in different areas. However, all models deviate from reality. Uncertainty quantification (UQ) process evaluates the overall uncertainties associated with the prediction of quantities of interest. In particular it studies the propagation of input uncertainties to the outputs of the models so that confidence intervals can be provided for the simulation results. In the present work, a non-intrusive quadrature-based uncertainty quantification (QBUQ) approach is proposed. The probability distribution function (PDF) of the system response can be then reconstructed using extended quadrature method of moments (EQMOM) and extended conditional quadrature method of moments (ECQMOM). The report first explains the theory of QBUQ approach, including methods to generate samples for problems with single or multiple uncertain input parameters, low order statistics, and required number of samples. Then methods for univariate PDF reconstruction (EQMOM) and multivariate PDF reconstruction (ECQMOM) are explained. The implementation of QBUQ approach into the open-source CFD code MFIX is discussed next. At last, QBUQ approach is demonstrated in several applications. The method is first applied to two examples: a developing flow in a channel with uncertain viscosity, and an oblique shock problem with uncertain upstream Mach number. The error in the prediction of the moment response is studied as a function of the number of samples, and the accuracy of the moments required to reconstruct the PDF of the system response is discussed. The QBUQ approach is then demonstrated by considering a bubbling fluidized bed as example application. The mean particle size is assumed to be the uncertain input parameter. The system is simulated with a standard two-fluid model with kinetic theory closures for the particulate phase implemented into MFIX. The effect of uncertainty on the disperse-phase volume fraction, on the phase velocities and on the pressure drop inside the fluidized bed are examined, and the reconstructed PDFs are provided for the three quantities studied. Then the approach is applied to a bubbling fluidized bed with two uncertain parameters, particle-particle and particle-wall restitution coefficients. Contour plots of the mean and standard deviation of solid volume fraction, solid phase velocities and gas pressure are provided. The PDFs of the response are reconstructed using EQMOM with appropriate kernel density functions. The simulation results are compared to experimental data provided by the 2013 NETL small-scale challenge problem. Lastly, the proposed procedure is demonstrated by considering a riser of a circulating fluidized bed as an example application. The mean particle size is considered to be the uncertain input parameter. Contour plots of the mean and standard deviation of solid volume fraction, solid phase velocities, and granular temperature are provided. Mean values and confidence intervals of the quantities of interest are compared to the experiment results. The univariate and bivariate PDF reconstructions of the system response are performed using EQMOM and ECQMOM.

97 MATHEMATICS AND COMPUTING↗

Meteorological services annual data report for 2015

This document presents the meteorological data collected at Brookhaven National Laboratory (BNL) by Meteorological Services (Met Services) for the calendar year 2015. The purpose is to publicize the data sets available to emergency personnel, researchers and facility operations. Met services has been collecting data at BNL since 1949. Data from 1994 to the present is available in digital format. Data is presented in monthly plots of one-minute data. This allows the reader the ability to peruse the data for trends or anomalies that may be of interest to them. Full data sets are available to BNL personnel and to a limited degree outside researchers. The full data sets allow plotting the data on expanded time scales to obtain greater details (e.g., daily solar variability, inversions, etc.).

54 ENVIRONMENTAL SCIENCES↗

Meteorological services annual data report for 2016

This document presents the meteorological data collected at Brookhaven National Laboratory (BNL) by Meteorological Services (Met Services) for the calendar year 2016. The purpose is to publicize the data sets available to emergency personnel, researchers and facility operations. Met services has been collecting data at BNL since 1949. Data from 1994 to the present is available in digital format. Data is presented in monthly plots of one-minute data. This allows the reader the ability to peruse the data for trends or anomalies that may be of interest to them. Full data sets are available to BNL personnel and to a limited degree outside researchers. The full data sets allow plotting the data on expanded time scales to obtain greater details (e.g., daily solar variability, inversions, etc.).

54 ENVIRONMENTAL SCIENCES↗

SURF Model Calibration Strategy

SURF and SURFplus are high explosive reactive burn models for shock initiation and propagation of detonation waves. They are engineering models motivated by the ignition & growth concept of high spots and for SURFplus a second slow reaction for the energy release from carbon clustering. A key feature of the SURF model is that there is a partial decoupling between model parameters and detonation properties. This enables reduced sets of independent parameters to be calibrated sequentially for the initiation and propagation regimes. Here we focus on a methodology for tting the initiation parameters to Pop plot data based on 1-D simulations to compute a numerical Pop plot. In addition, the strategy for tting the remaining parameters for the propagation regime and failure diameter is discussed.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

External Threat Risk Assessment Algorithm (ExTRAA)

Two risk assessment algorithms and philosophies have been augmented and combined to form a new algorit hm, the External Threat Risk Assessment Algorithm (ExTRAA), that allows for effective and statistically sound analysis of external threat sources in relation to individual attack methods . In addition to the attack method use probability and the attack method employment consequence, t he concept of defining threat sources is added to the risk assessment process. Sample data is tabulated and depicted in radar plots and bar graphs for algorithm demonstration purposes. The largest success of ExTRAA is its ability to visualize the kind of r isk posed in a given situation using the radar plot method.

97 MATHEMATICS AND COMPUTING↗

Accelerated Climate Modeling For Energy

This is the final report on the work of the New York University team to the DOE Accelerated Climate Modeling For Energy (ACME) project. NYU was one of the original developers of the UV-CDAT tool for climate data analysis, which is being used in ACME. NYU primarily focused on the analysis package graphical user interface, workflow and provenance functionality. The most significant activities in the last year of the grant were the development of the new plotting system in UVCMetrics package and the package EzLinePlot for 1D plots which are described in detail.

54 ENVIRONMENTAL SCIENCES↗