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DOE OSTI2011

Invasion triangle: an organizational framework for species invasion: Invasion Triangle

Species invasion is a complex, multifactor process. To encapsulate this complexity into an intuitively appealing, simple, and straightforward manner, we present an organizational framework in the form of an invasion triangle. The invasion triangle is an adaptation of the disease triangle used by plant pathologists to help envision and evaluate interactions among a host, a pathogen, and an environment. Our modification of this framework for invasive species incorporates the major processes that result in invasion as the three sides of the triangle: (1) attributes of the potential invader; (2) biotic characteristics of a potentially invaded site; and (3) environmental conditions of the site. The invasion triangle also includes the impact of external influences on each side of the triangle, such as climate and land use change. This paper introduces the invasion triangle, discusses how accepted invasion hypotheses are integrated in this framework, describes how the invasion triangle can be used to focus research and management, and provides examples of application. The framework provided by the invasion triangle is easy to use by both researchers and managers and also applicable at any level of data intensity, from expert opinion to highly controlled experiments. The organizational framework provided by the invasion triangle is beneficial for understanding and predicting why species are invasive in specific environments, for identifying knowledge gaps, for facilitating communication, and for directing management in regard to invasive species.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Relating flow resistance to equivalent roughness

Describing flow resistance using the physical properties of an underlying surface is a recalcitrant problem in overland flow models. If discharge measurements are available, an equivalent roughness (e.g., Manning’s n) can be calibrated to represent the effects of surface properties within the domain with a single numerical value. Alternatively, the flow resistance can be estimated from discharge and velocity measured at a point, typically a runoff plot outlet. However, such experimental estimates are often inconsistent with the equivalent roughness determined from calibration to discharge, even if both derive from the same dataset. For example, if Manning’s equation is used to parameterize flow resistance, the Manning’s n obtained by calibrating a model to discharge differs from the value of n calculated from measured flow and velocity at the hillslope outlet. Here, this discrepancy is resolved by deriving a correction factor relating experimentally-determined flow resistance to the equivalent roughness. The derived correction factor is tested for four commonly-used resistance formulations using 129 rainfall simulator experiments. The correction factor is necessary to reproduce measured velocities, and yields minor improvements in discharge prediction. Plain Language Summary: Accurate runoff prediction is needed for land and water management in dryland regions, where sporadic and limited rainfall necessitate efficient water use and drought mitigation strategies. The skill of runoff models is known to be hindered by out ability to estimate flow resistance, which is the quantity that describes how energy is lost from flowing water to the underlying surface. Typically, models represent flow resistance with an equivalent roughness, e.g., Manning’s n, that is adjusted until the model can reproduce available discharge observations at watershed scale. However, the flow resistance measured in plot-scale experiments (1–10 m) often exceeds equivalent roughness coefficients by a factor of 10. This means that the direct use of plot-scale experimental data to parameterize runoff models could cause errors in discharge and runoff velocity predictions. Here, we resolve these differences by deriving an analytic correction factor that relates flow resistance to the equivalent roughness required for models to reproduce experimental velocity and discharge data. This correction factor is tested using rainfall simulator data from 129 experiments performed in the US Southwest covering a wide range of precipitation intensities, soil textures and vegetation types. Use of the correction factor substantially improves model prediction of flow velocity, which is needed for reproducing the timing of flood events and the estimation of erosion.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Polarimetry diagnostic on OMEGA EP using a 10-ps, 263-nm probe beam

A polarimetry diagnostic was built and characterized for magnetic-field measurements in laser-plasma experiments on the OMEGA EP laser. This diagnostic was built into the existing 4ω (263-nm) probe system that employs a 10-ps laser pulse collected with an f/4 imaging system. The diagnostic measures the rotation of the probe beam's polarization. The polarimeter uses a Wollaston prism to split the probe beam into orthogonal polarization components. Spatially localized intensity variations between images indicate polarization rotation. Magnetic fields can be calculated by combining the polarimetry data with the measured plasma density profile obtained from angular filter refractometry.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

Note: A novel normalization scheme for laser-based plasma x-ray sources

A kHz repetition rate laser pump-X-ray probe system for ultrafast X-ray diffraction is set up based on a laser-driven plasma X-ray source. A simple and reliable normalization approach has been developed to minimize the impact of large X-ray pulse intensity fluctuation on data quality. It utilizes one single X-ray area detector to record both sample and reference signals simultaneously. Performance of this novel normalization method is demonstrated in reflectivity oscillation measurement of a superlattice sample at sub-ps resolution.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

High phase resolution: Probing interactions in complex interfaces with sum frequency generation

An often-quoted statement attributed to Wolfgang Pauli is that God made the bulk, but the surface was invented by the devil. Although humorous, the statement really reflects frustration in developing a detailed picture of a surface. In the last several decades, that frustration has begun to abate with numerous techniques providing clues to interactions and reactions at surfaces. Often these techniques require considerable prior knowledge. Complex mixtures on irregular or soft surfaces—complex interfaces—thus represent the last frontier. Two optical techniques: sum frequency generation (SFG) and second harmonic generation (SHG) are beginning to lift the veil on complex interfaces. Of these techniques, SFG with one excitation in the infrared has the potential to provide exquisite molecular- and moiety-specific vibrational data. This Perspective is intended both to aid newcomers in gaining traction in this field and to demonstrate the impact of high-phase resolution. It starts with a basic description of light-induced surface polarization that is at the heart of SFG. The sum frequency is generated when the input fields are sufficiently intense that the interaction is nonlinear. This nonlinearity represents a challenge for disentangling data to reveal the molecular-level picture. Three, high-phase-resolution methods that reveal interactions at the surface are described.

Biophysics↗

DOE OSTI2015

Data Exploration Toolkit for serial diffraction experiments

This paper describes a set of tools allowing experimentalists insight into the variation present within large serial data sets. Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the ‘diffraction before destruction’ nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Final Report on DTRA Basic Research Project #BRCALL08-Per3-C-2-0006 "High-Z Non-Equilibrium Physics and Bright X-ray Sources with New Laser Targets"

This project had two major goals. Final Goal: obtain spectrally resolved, absolutely calibrated x-ray emission data from uniquely uniform mm-scale near-critical-density high-Z plasmas not in local thermodynamic equilibrium (LTE) to benchmark modern detailed atomic physics models. Scientific significance: advance understanding of non-LTE atomic physics. Intermediate Goal: develop new nano-fabrication techniques to make suitable laser targets that form the required highly uniform non-LTE plasmas when illuminated by high-intensity laser light. Scientific significance: advance understanding of nano-science. The new knowledge will allow us to make x-ray sources that are bright at the photon energies of most interest for testing radiation hardening technologies, the spectral energy range where current x-ray sources are weak. All project goals were met.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2013

High-Z Non-Equilibrium Physics and Bright X-ray Sources with New Laser Targets (Annual Report FY 2013)

This project has two major goals, as follows, Final Goal: obtain spectrally resolved, absolutely calibrated x-ray emission data from uniquely uniform mm-scale near-critical-density high-Z plasmas not in local thermodynamic equilibrium (LTE) to benchmark modern detailed atomic physics models. Scientific significance: advance understanding of non-LTE atomic physics. Intermediate Goal: develop new nano-fabrication techniques to make suitable laser targets that form the required highly uniform non-LTE plasmas when illuminated by high-intensity laser light. Scientific significance: advance understanding of nano-science. Relation to DTRA C-WMD mission: The new knowledge will allow us to make x-ray sources that are bright at the photon energies of most interest for testing radiation hardening technologies, the spectral energy range where current x-ray sources are weak.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Total absorption {gamma}-ray spectroscopy of beta delayed neutron emitters

Preliminary results of the data analysis of the beta decay of {sup 94}Rb using a novel - segmented- total absorption spectrometer are shown in this contribution. This result is part of a systematic study of important contributors to the decay heat problem in nuclear reactors. In this particular case the goal is to determine the beta intensity distribution below the neutron separation energy and the gamma/beta competition above.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Classification Analysis of Southwest Pacific Tropical Cyclone Intensity Changes Prior to Landfall

This study evaluates the ability of a random forest classifier to identify tropical cyclone (TC) intensification or weakening prior to landfall over the western region of the Southwest Pacific Ocean (SWPO) basin. For both Australia mainland and SWPO island cases, when a TC first crosses land after spending ≥24 h over the ocean, the closest hour prior to the intersection is considered as the landfall hour. If the maximum wind speed (V max ) at the landfall hour increased or remained the same from the 24-h mark prior to landfall, the TC is labeled as intensifying and if the V max at the landfall hour decreases, the TC is labeled as weakening. Geophysical and aerosol variables closest to the 24 h before landfall hour were collected for each sample. The random forest model with leave-one-out cross validation and the random oversampling example technique was identified as the best-performing classifier for both mainland and island cases. The model identified longitude, initial intensity, and sea skin temperature as the most important variables for the mainland and island landfall classification decisions. Incorrectly classified cases from the test data were analyzed by sorting the cases by their initial intensity hour, landfall hour, monthly distribution, and 24-h intensity changes. TC intensity changes near land strongly impact coastal preparations such as wind damage and flood damage mitigations; hence, this study will contribute to improve identifying and prioritizing prediction of important variables contributing to TC intensity change before landfall.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

ACT University Collaboration Proposal: Role of manufacturing defects on material failure under dynamic loading for developing enhanced failure models and theories (Final Report)

Research on the tensile behavior of additively manufactured 316L stainless steel coupon specimens at increasing strain rates was conducted over the past year at Penn State. Dynamic loading rates into the 1000 1/s loading rates were performed on specimens with nearly 1.32” gage lengths. Stress-strain plots show ductile and plastic behavior well beyond 12% strain with necked specimens, having smaller effective gage lengths showing up to 56% ultimate strain. Additional tests performed on compact tension specimens helped with simulation work to understand the deformation behavior. Using finite elements, it was possible to determine the feasibility of a comprehensive experimental validation study towards an improved model for AM material failure – specifically, the Bai-Wierzbicki approach which accounts for lode angle and triaxiality. A non-significant number of tests are projected for eight specific failure nodes, with additional replicates to provide strain-rate capabilities to the existing formulation. One such correction factor is explored for quasi-static, notched specimens. Finally, stress intensity factor was explored using a set of compact-tension specimens which would also provide useful validation data for any simulation work.

36 MATERIALS SCIENCE↗

NASA NTRS1999

Tracker: Image-Processing and Object-Tracking System Developed

Tracker is an object-tracking and image-processing program designed and developed at the NASA Lewis Research Center to help with the analysis of images generated by microgravity combustion and fluid physics experiments. Experiments are often recorded on film or videotape for analysis later. Tracker automates the process of examining each frame of the recorded experiment, performing image-processing operations to bring out the desired detail, and recording the positions of the objects of interest. It can load sequences of images from disk files or acquire images (via a frame grabber) from film transports, videotape, laser disks, or a live camera. Tracker controls the image source to automatically advance to the next frame. It can employ a large array of image-processing operations to enhance the detail of the acquired images and can analyze an arbitrarily large number of objects simultaneously. Several different tracking algorithms are available, including conventional threshold and correlation-based techniques, and more esoteric procedures such as "snake" tracking and automated recognition of character data in the image. The Tracker software was written to be operated by researchers, thus every attempt was made to make the software as user friendly and self-explanatory as possible. Tracker is used by most of the microgravity combustion and fluid physics experiments performed by Lewis, and by visiting researchers. This includes experiments performed on the space shuttles, Mir, sounding rockets, zero-g research airplanes, drop towers, and ground-based laboratories. This software automates the analysis of the flame or liquid s physical parameters such as position, velocity, acceleration, size, shape, intensity characteristics, color, and centroid, as well as a number of other measurements. It can perform these operations on multiple objects simultaneously. Another key feature of Tracker is that it performs optical character recognition (OCR). This feature is useful in extracting numerical instrumentation data that are embedded in images. All the results are saved in files for further data reduction and graphing. There are currently three Tracking Systems (workstations) operating near the laboratories and offices of Lewis Microgravity Science Division researchers. These systems are used independently by students, scientists, and university-based principal investigators. The researchers bring their tapes or films to the workstation and perform the tracking analysis. The resultant data files generated by the tracking process can then be analyzed on the spot, although most of the time researchers prefer to transfer them via the network to their offices for further analysis or plotting. In addition, many researchers have installed Tracker on computers in their office for desktop analysis of digital image sequences, which can be digitized by the Tracking System or some other means. Tracker has not only provided a capability to efficiently and automatically analyze large volumes of data, saving many hours of tedious work, but has also provided new capabilities to extract valuable information and phenomena that was heretofore undetected and unexploited.

Klimek, Robert B.↗

DOE OSTI2021

Urban Energy Systems: Research at Oak Ridge National Laboratory

In the coming decades, our planet will witness unprecedented urban population growth in both established and emerging communities. The development and maintenance of urban infrastructures are highly energy-intensive. Urban areas are dictated by complex intersections among physical, engineered, and human dimensions that have significant implications for traffic congestion, emissions, and energy usage. In this chapter, we highlight recent research and development efforts at Oak Ridge National Laboratory (ORNL), the largest multipurpose science laboratory within the U.S. Department of Energy’s (DOE) national laboratory system, that characterizes the interactions between the human dynamics and critical infrastructures in conjunction with the integration of four distinct components: data, critical infrastructure models, and scalable computation and visualization, all within the context of physical and social systems. Discussions focus on four key topical themes: population and land use, sustainable mobility, the energy-water nexus, and urban resiliency, that are mutually aligned with DOE’s mission and ORNL’s signature science and technology capabilities. Using scalable computing, data visualization, and unique datasets from a variety of sources, the institute fosters innovative interdisciplinary research that integrates ORNL expertise in critical infrastructures including energy, water, transportation, and cyber, and their interactions with the human population.

Bhaduri, Budhu↗

DOE OSTI2010

Inelastic and Quasielastic Neutron Scattering in PbMg1/3Nb2/3O3 Above the Burns Temperature

We present here the results of the study of the true paraelectric phase of PMN via neutron inelastic and quasielastic scattering. Inelastic data for two different Brillouin Zones were treated simultaneously in terms of the 2-mode approach for the lowest TO mode. We have confirmed that 2-mode description allows removing the contradictions between the temperature dependences of the soft-mode frequency and the dielectric susceptibility existing in the single mode model. The diffuse scattering was mapped in three Brillouin zones and substantial anisotropy of the 2-d intensity distribution was found that was not reported before. Treatment of data in terms of Huang scattering produced satisfactory description of the experimental data. It is shown that broad satellite peaks close to the main Bragg reflections in our case can be described in terms of instrumental resolution.

36 MATERIALS SCIENCE↗

DOE OSTI2010

Recovering magnetization distributions from their noisy diffraction data

We study, using simulated experiments inspired by thin-film magnetic domain patterns, the feasibility of phase retrieval in x-ray diffractive imaging in the presence of intrinsic charge scattering given only photon-shot-noise limited diffraction data. We detail a reconstruction algorithm to recover the sample's magnetization distribution under such conditions and compare its performance with that of Fourier transform holography. Concerning the design of future experiments, we also chart out the reconstruction limits of diffractive imaging when photon-shot-noise and the intensity of charge scattering noise are independently varied. This work is directly relevant to the time-resolved imaging of magnetic dynamics using coherent and ultrafast radiation from x-ray free-electron lasers and also to broader classes of diffractive imaging experiments which suffer noisy data, missing data, or both.

36 MATERIALS SCIENCE↗

NASA NTRS2011

Accelerated Adaptive MGS Phase Retrieval

The Modified Gerchberg-Saxton (MGS) algorithm is an image-based wavefront-sensing method that can turn any science instrument focal plane into a wavefront sensor. MGS characterizes optical systems by estimating the wavefront errors in the exit pupil using only intensity images of a star or other point source of light. This innovative implementation of MGS significantly accelerates the MGS phase retrieval algorithm by using stream-processing hardware on conventional graphics cards. Stream processing is a relatively new, yet powerful, paradigm to allow parallel processing of certain applications that apply single instructions to multiple data (SIMD). These stream processors are designed specifically to support large-scale parallel computing on a single graphics chip. Computationally intensive algorithms, such as the Fast Fourier Transform (FFT), are particularly well suited for this computing environment. This high-speed version of MGS exploits commercially available hardware to accomplish the same objective in a fraction of the original time. The exploit involves performing matrix calculations in nVidia graphic cards. The graphical processor unit (GPU) is hardware that is specialized for computationally intensive, highly parallel computation. From the software perspective, a parallel programming model is used, called CUDA, to transparently scale multicore parallelism in hardware. This technology gives computationally intensive applications access to the processing power of the nVidia GPUs through a C/C++ programming interface. The AAMGS (Accelerated Adaptive MGS) software takes advantage of these advanced technologies, to accelerate the optical phase error characterization. With a single PC that contains four nVidia GTX-280 graphic cards, the new implementation can process four images simultaneously to produce a JWST (James Webb Space Telescope) wavefront measurement 60 times faster than the previous code.

Lam, Raymond K.↗

NASA NTRSDate not supplied

Merging Analytic Collaborative Frameworks with New Observing Strategies Toward a Digital Twin: Earth – Episodic Pulse Event Impacts on Ocean Carbon Cycle as an Example

Virtual representations of the Earth will allow us to address some of the most critical environmental issues of our time. Here, we show the first steps toward representation of riverine, estuarine, and coastal carbon processes to enable scenario driven “what-if” analyses of the carbon system and human footprint. Excess sediment and nutrient runoff from land-based human activities impact water quality and can pose serious threats to coastal and marine ecosystems. Episodic pulse events, such as extreme precipitation events, can increase the amount of nutrients entering estuaries and coastal regions, potentially leading to large phytoplankton blooms followed by anoxic conditions. Consequences of coastal runoff are predicted to increase with the higher intensity and frequency of extreme events. Beyond the threat to coastal ecosystems, recent findings suggest these episodic pulses might play a significant role for biological production influencing regional and global carbon fluxes and budgets. An improved understanding of these events through optimal, dynamic observing strategies will increase our knowledge of the land-ocean continuum and how regional events and nutrient fluxes affect the carbon cycle and ocean ecosystem. This conceptual framework enables focused science investigations by pairing data analytics and artificial intelligence tools (otherwise termed an Analytic Center Framework, ACF) with targeted measurement acquisition through distributed sensing and intelligent asset tasking (or New Observing Strategies, NOS). This NOS and ACF iterative approach acquires and integrates complementary and coincident satellite, in-situ and model data to build a more complete and in-depth picture of science phenomena. Specifically, Apache Science Data Analytic Platform (SDAP) is extended to incorporate relevant datasets for data access, harmonized analysis, and anomaly detection. When conditions are met for a likely pulse event, NASA’s D-SHIELD (Distributed Spacecraft with Heuristic Intelligence to Enable Logistical Decisions) tool is triggered to optimize asset overpass frequency and schedule observations for persistent monitoring. Targeted data is ingested by SDAP for enhanced investigation via iterative analysis until the trigger criteria is no longer met - steps toward a digital twin.

Laura Rogers↗