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At least 1,063 records · Page 59

Temporal Patterns in Soil Redox Potential Vary Across a Freshwater Coastal Delta

Widespread and persistent flooding is submerging coastal ecosystems, particularly along the Louisiana Gulf coast, where flooding results from the compounding effects of ground subsidence and rising sea level. Restoration projects aim to mitigate land loss by diverting sediment loads from rivers into degraded areas to increase ground elevation. To predict how coastal ecosystems will change over time in response to projected changes in relative sea level and restoration, it is necessary to understand how subsurface biogeochemical processes respond to dynamic hydrologic forcings. Here, this study evaluates how environmental parameters that integrate biogeochemical processes vary with water table fluctuations in the freshwater Wax Lake Delta (WLD) in Louisiana, USA, where water diversions have formed one of the only active deltas along the coast. High‐frequency observations of water level, soil redox potential, specific conductance and pH were made for 1 year along elevation transects located on the older, proximal and younger, distal ends of a deltaic island. Redox responded rapidly to changing water tables, with fluctuations occurring primarily in shallow soils (< 20 cm) and at higher elevations. Deeper soils and those at lower elevation remained inundated and reduced. Semi‐diurnal tidal fluctuations were pronounced in younger, distal soils, presumably due to rapid groundwater exchange with the river channel. Tidal signals were muted in older soils that instead exhibited seasonal variability associated with river discharge and evapotranspiration. Although much of the delta sediments are persistently reducing and anoxic, redox fluctuations in the natural levees that border the deltaic islands likely drive high rates of biogeochemical activity. Evaluating how hydrology drives the frequency and duration of redox fluctuations provides a basis for understanding how biogeochemical processes might vary with complex hydrological interactions in coastal systems.

Herndon, Elizabeth [Oak Ridge National Laboratory ↗

Enhancing Network Visibility and Security through Tensor Analysis

The increasing size, variety, rate of growth and change, and complexity of network data has warranted advanced network analysis and services. Tools that provide automated analysis through traditional or advanced signature-based systems or machine learning classifiers suffer from practical difficulties. These tools fail to provide comprehensive and contextual insights into the network when put to practical use in operational cyber security. In this paper, we present an effective tool for network security and traffic analysis that uses high-performance data analytics based on a class of unsupervised learning algorithms called tensor decompositions. The tool aims to provide a scalable analysis of the network traffic data and also reduce the cognitive load of network analysts and be network-expert-friendly by presenting clear and actionable insights into the network. With this being said, In this paper, we demonstrate the successful use of the tool in two completely diverse operational cyber security environments, namely, (1) security operations center (SOC) for the SCinet network at the SuperComputing (SC) Conference in 2016 and 2017 and (2) Reservoir Labs’ Local Area Network (LAN). In each of these environments, we produce actionable results for cyber security specialists including (but not limited to) (1) finding malicious network traffic involving internal and external attackers using port scans, SSH brute forcing, and NTP amplification attacks, (2) uncovering obfuscated network threats such as data exfiltration using DNS port and using ICMP traffic, and (3) finding network misconfiguration and performance degradation patterns.

97 MATHEMATICS AND COMPUTING↗

Solid Freeform Fabrication of Composite-Material Objects

Composite solid freeform fabrication (C-SFF) or composite layer manufacturing (CLM) is an automated process in which an advanced composite material (a matrix reinforced with continuous fibers) is formed into a freestanding, possibly complex, three-dimensional object. In CLM, there is no need for molds, dies, or other expensive tooling, and there is usually no need for machining to ensure that the object is formed to the desired net size and shape. CLM is a variant of extrusion-type rapid prototyping, in which a model or prototype of a solid object is built up by controlled extrusion of a polymeric or other material through an orifice that is translated to form patterned layers. The second layer is deposited on top of the first layer, the third layer is deposited on top of the second layer, and so forth, until the stack of layers reaches the desired final thickness and shape. The elements of CLM include (1) preparing a matrix resin in a form in which it will solidify subsequently, (2) mixing the fibers and matrix material to form a continuous pre-impregnated tow (also called "towpreg"), and (3) dispensing the pre-impregnated tow from a nozzle onto a base while moving the nozzle to form the dispensed material into a patterned layer of controlled thickness. When the material deposited into a given layer has solidified, the material for the next layer is deposited and patterned similarly, and so forth, until the desired overall object has been built up as a stack of patterned layers. Preferably, the deposition apparatus is controlled by a computer-aided design (CAD) system. The basic CLM concept can be adapted to the fabrication of parts from a variety of matrix materials. It is conceivable that a CLM apparatus could be placed at a remote location on Earth or in outer space where (1) spare parts are expected to be needed but (2) it would be uneconomical or impractical to store a full inventory of spare parts. A wide variety of towpregs could be prepared and stored on spools until needed. Long-shelf-life towpreg materials suitable for such use could include thermoplastic-coated carbon fibers and metal-coated SiC fibers. When a spare part was needed, the part could be fabricated by CLM under control by a CAD data file; thus, the part could be built automatically, at the scene, within hours or minutes.

Wang, C. Jeff↗

A gradient-based deep neural network model for simulating multiphase flow in porous media

We report simulation of multiphase flow in porous media is crucial for the effective management of subsurface energy and environment-related activities. The numerical simulators used for modeling such processes rely on spatial and temporal discretization of the governing mass and energy balance partial-differential equations (PDEs) into algebraic systems via finite-difference/volume/element methods. These simulators usually require dedicated software development and maintenance, and suffer low efficiency from a runtime and memory standpoint for problems with multi-scale heterogeneity, coupled-physics processes or fluids with complex phase behavior. Therefore, developing cost-effective, data-driven models can become a practical choice, and in this work, we choose deep learning approaches as they can handle high dimensional data and accurately predict state variables with strong nonlinearity. In this paper, we describe a gradient-based deep neural network (GDNN) constrained by the physics related to multiphase flow in porous media. We tackle the nonlinearity of flow in porous media induced by rock heterogeneity, fluid properties, and fluid-rock interactions by decomposing the nonlinear PDEs into a dictionary of elementary differential operators. We use a combination of operators to handle rock spatial heterogeneity and fluid flow by advection. Since the augmented differential operators are inherently related to the physics of fluid flow, we treat them as first principles prior knowledge to regularize the GDNN training. We use the example of pressure management at geologic CO 2 storage sites, where CO 2 is injected in saline aquifers and brine is produced, and apply GDNN to construct a predictive model that is trained with physics-based simulation data and emulates the physics process. We demonstrate that GDNN can effectively predict the nonlinear patterns of subsurface responses, including the temporal and spatial evolution of the pressure and saturation plumes. We also successfully extend the GDNN to convolutional neural network (CNN), namely gradient-based CNN (GCNN), and validate its capability to improve the prediction accuracy. GDNN has great potential to tackle challenging problems that are governed by highly nonlinear physics and enable the development of data-driven models with higher fidelity.

42 ENGINEERING↗

Characteristics of the field-aligned current system in the nighttime sector during auroral substorms

Fujii et al. (1994) obtained characteristics of the electrodynamic parameters, that is, field-aligned currents, electric fields, and electron precipitation, which are associted with auroral substorm events in the nighttime sector, through a unique analysis that places the ionospheric measurements of these parameters into the context of a generic substorm determined from global auroral images. In this paper we investigate in considerably more detail the characteristics of the field-aligned currents using data from the same set of passes as the previuos study. We show for the first time that the net upward field-aligned currents throughout the surge and surge horn are sufficient to account for most if not all of the converging currents of the auroral electrojets. Current densities are largest in the surge and surge horn. Current region continuity does not appear to exist across the substorm bulge region. Much of the auroral substorm field-aligned current is composed of filamentary currents and finite current segments at large angles to each other. The westward electrojet may contain large gradients in intensity both in local time and latitude due to sets of localized field-aligned currents. The net downward current for several hours to the west of the surge is insufficient to account for the eastward electrojet, consistent with the concept that this electrojet originates primarily on the dayside. Our pattern of field-aligned currents associated with the surge has common features and also differs significantly from the patterns previously derived from data from radars and ground-based magnetometer arrays. Our pattern is considerably more complex, probably due to the much higher resolution in latitude of the satellite data. It is also larger in area, since our average substorm is much larger than those pertaining to the previous patterns, giving a substorm wedge considerably wider than that obtained from the radar and array data.

Hoffman, R. A.↗

Strain evolution in Zr-2.5 wt% Nb observed with synchrotron X-ray diffraction

Highlights: • The X-ray diffraction is useful for in-situ monitoring of lattice strain thermal changes in differently oriented grains. • 2D elastic strain evaluation performed for α-matrix and for δ-hydride. • A change in matrix strain considered as a sum of metal thermal expansion, effect of hydrogen, and inter-granular strain. • Differently oriented hydrides have different lattice parameter and start from different strain states. The mechanical behaviour of hydrides in Zr alloy at low hydrogen concentrations continues to be the subject of research due to wide engineering application and highly complex behaviour of the Zr-H system. Significant structural differences between hydrides and α-Zr cause large dilatational strains associated with formation of the hydride precipitates in zirconium. Two hydride populations were observed to form under different strain states in the α-Zr matrix. The hysteresis of the hydrogen solubility is detected both in intensity and in strain curves for measured δ(111), α(00.2) and α{10.0} peaks. A two-dimensional analysis of α-strain was performed for the axial-hoop, hoop-radial, and axial-radial planes of Zr-2.5 wt% Nb pressure tube material. Variations in the hydrostatic and deviatoric strain components of the α-Zr with temperature were examined. In addition, a change in phase strain during a thermal excursion was considered as a sum of three cooperating components: phase thermal expansion (ε{sub T}), strains associated with other phase presenting in material (ε{sub [H]} or ε{sub matrix}), and inter-granular strain within the phase caused by Type II stresses (ε{sub other}). The present study broadens our understanding of strain evolution in a Zr-H system undergoing hydride dissolution and precipitation. An X-ray synchrotron diffraction technique enables the in-situ following of strain variations in differently oriented grain families during the thermal cycle. In contrast to widely reported the average strain value within the α-phase, the diffraction patterns generated with this technique allow the evaluation of the anisotropic directionality of strains in different phases in Zr-H system generated during phase transformation.

36 MATERIALS SCIENCE↗

Performance Validation of Pulsed Thermal Imaging System for In-Service Applications

Additive manufacturing (AM) is an emerging method for cost-efficient fabrication of complex topology nuclear reactor parts from high-strength corrosion resistance alloys, such as stainless steel and Inconel. AM of metallic structures for nuclear energy applications is currently based on laser powder bed fusion (LPBF) process, which has the capability of melting metallic powder and net shaping the structures with relatively high precision. Some of the challenges with using LPBF method for nuclear manufacturing include the possibility of introducing pores into metallic structures. Integrity of AM structures needs to be evaluated nondestructively because material flaws could lead to premature failures in high temperature nuclear reactor environment. Currently, there exist limited capabilities to evaluate actual AM structures non-destructively. Pulsed Thermography Imaging (PTI) provides a capability for non-destructive evaluation (NDE) of subsurface defects in arbitrary size structures. The PTI method is based on recording material surface temperature transients with infrared (IR) camera following thermal pulse delivered on material surface with flash light. The PTI method has advantages for NDE of actual AM structures because the method involves one-sided non-contact measurements and fast processing of large sample areas captured in one image. Following initial qualification of an AM component for deployment in a nuclear reactor, a PTI system can also be used for in-service nondestructive evaluation (NDE) applications. In this report, we describe recent progress in enhancing PTI capabilities in detecting microscopic defects in metallic specimens. SS316 and IN718 specimens were developed with a pattern of subsurface calibrated flat bottom hole (FBH) defects with diameters from 500µm to 200µm. FBH’s were created with EDM (electron discharge machining) drill. PTI imaging data was processed Spatial Temporal Denoised Thermal Source Separation (STDTSS) unsupervised machine learning (ML) algorithm. We show that defects as small as 200µm in SS316 and IN718 can be detected with STDTSS algorithm. To the best of our knowledge, these are the smallest detected defects which are reported in literature.

42 ENGINEERING↗

Reaching during virtual rotation: context specific compensations for expected coriolis forces

Subjects who are in an enclosed chamber rotating at constant velocity feel physically stationary but make errors when pointing to targets. Reaching paths and endpoints are deviated in the direction of the transient inertial Coriolis forces generated by their arm movements. By contrast, reaching movements made during natural, voluntary torso rotation seem to be accurate, and subjects are unaware of the Coriolis forces generated by their movements. This pattern suggests that the motor plan for reaching movements uses a representation of body motion to prepare compensations for impending self-generated accelerative loads on the arm. If so, stationary subjects who are experiencing illusory self-rotation should make reaching errors when pointing to a target. These errors should be in the direction opposite the Coriolis accelerations their arm movements would generate if they were actually rotating. To determine whether such compensations exist, we had subjects in four experiments make visually open-loop reaches to targets while they were experiencing compelling illusory self-rotation and displacement induced by rotation of a complex, natural visual scene. The paths and endpoints of their initial reaching movements were significantly displaced leftward during counterclockwise illusory rotary displacement and rightward during clockwise illusory self-displacement. Subjects reached in a curvilinear path to the wrong place. These reaching errors were opposite in direction to the Coriolis forces that would have been generated by their arm movements during actual torso rotation. The magnitude of path curvature and endpoint errors increased as the speed of illusory self-rotation increased. In successive reaches, movement paths became straighter and endpoints more accurate despite the absence of visual error feedback or tactile feedback about target location. When subjects were again presented a stationary scene, their initial reaches were indistinguishable from pre-exposure baseline, indicating a total absence of aftereffects. These experiments demonstrate that the nervous system automatically compensates in a context-specific fashion for the Coriolis forces associated with reaching movements.

Clinical Trial↗

In Situ Inference for Earth System Predictability

Focal Area: Focal Area 3: Insight gleaned from complex simulated data using AI, big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI. Science Challenge: An understanding of future evolution in precipitation extremes is critical to numerous DOE mission questions. Extreme events are by nature short time-scale events that are difficult to diagnose in available model data. Accurate modeling of extreme events necessarily requires high spatial resolution at the storm scale locally. However, the environment in which storms grow is dependent on global, remote, processes. These complex spatiotemporal relationships are impossible to diagnose at resolutions required to accurately model storms responsible for extreme precipitation. At exascale, climate simulations will produce results at fine enough resolution to investigate these relationships. However, the resulting data from these simulations will be far too large to save for post-simulation analysis. We advocate for fitting statistical models inside the simulations as they run, a context known as in situ, which will facilitate scientific investigations using the full fine-scale data stream. Figure 1 shows an example of the type of model we could consider, a Bayesian hierarchical spatial regression model. Precipitation extremes at each grid cell are modeled using extreme value distributions. Since extremes are rare, fitting models to individual grid cells can result in high variance and poor estimates. Instead, the model can be made more robust by smoothing the parameters of the extreme value model across space. Additionally, the parameters themselves can be functionally linked to other variables elsewhere in the simulation. Thus, we can use the fine-scale data to build more robust models for extremes that link extreme behavior to other climate patterns.

54 ENVIRONMENTAL SCIENCES↗

NASA Tech Briefs, September 2006

Topics covered include: Improving Thermomechanical Properties of SiC/SiC Composites; Aerogel/Particle Composites for Thermoelectric Devices; Patches for Repairing Ceramics and Ceramic- Matrix Composites; Lower-Conductivity Ceramic Materials for Thermal-Barrier Coatings; An Alternative for Emergency Preemption of Traffic Lights; Vehicle Transponder for Preemption of Traffic Lights; Automated Announcements of Approaching Emergency Vehicles; Intersection Monitor for Traffic-Light-Preemption System; Full-Duplex Digital Communication on a Single Laser Beam; Stabilizing Microwave Frequency of a Photonic Oscillator; Microwave Oscillators Based on Nonlinear WGM Resonators; Pointing Reference Scheme for Free-Space Optical Communications Systems; High-Level Performance Modeling of SAR Systems; Spectral Analysis Tool 6.2 for Windows; Multi-Platform Avionics Simulator; Silicon-Based Optical Modulator with Ferroelectric Layer; Multiplexing Transducers Based on Tunnel-Diode Oscillators; Scheduling with Automated Resolution of Conflicts; Symbolic Constraint Maintenance Grid; Discerning Trends in Performance Across Multiple Events; Magnetic Field Solver; Computing for Aiming a Spaceborne Bistatic- Radar Transmitter; 4-Vinyl-1,3-Dioxolane-2-One as an Additive for Li-Ion Cells; Probabilistic Prediction of Lifetimes of Ceramic Parts; STRANAL-PMC Version 2.0; Micromechanics and Piezo Enhancements of HyperSizer; Single-Phase Rare-Earth Oxide/Aluminum Oxide Glasses; Tilt/Tip/Piston Manipulator with Base-Mounted Actuators; Measurement of Model Noise in a Hard-Wall Wind Tunnel; Loci-STREAM Version 0.9; The Synergistic Engineering Environment; Reconfigurable Software for Controlling Formation Flying; More About the Tetrahedral Unstructured Software System; Computing Flows Using Chimera and Unstructured Grids; Avoiding Obstructions in Aiming a High-Gain Antenna; Analyzing Aeroelastic Stability of a Tilt-Rotor Aircraft; Tracking Positions and Attitudes of Mars Rovers; Stochastic Evolutionary Algorithms for Planning Robot Paths; Compressible Flow Toolbox; Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines; General Flow-Solver Code for Turbomachinery Applications; Code for Multiblock CFD and Heat-Transfer Computations; Rotating-Pump Design Code; Covering a Crucible with Metal Containing Channels; Repairing Fractured Bones by Use of Bioabsorbable Composites; Kalman Filter for Calibrating a Telescope Focal Plane; Electronic Absolute Cartesian Autocollimator; Fiber-Optic Gratings for Lidar Measurements of Water Vapor; Simulating Responses of Gravitational-Wave Instrumentation; SOFTC: A Software Correlator for VLBI; Progress in Computational Simulation of Earthquakes; Database of Properties of Meteors; Computing Spacecraft Solar-Cell Damage by Charged Particles; Thermal Model of a Current-Carrying Wire in a Vacuum; Program for Analyzing Flows in a Complex Network; Program Predicts Performance of Optical Parametric Oscillators; Processing TES Level-1B Data; Automated Camera Calibration; Tracking the Martian CO2 Polar Ice Caps in Infrared Images; Processing TES Level-2 Data; SmaggIce Version 1.8; Solving the Swath Segment Selection Problem; The Spatial Standard Observer; Less-Complex Method of Classifying MPSK; Improvement in Recursive Hierarchical Segmentation of Data; Using Heaps in Recursive Hierarchical Segmentation of Data; Tool for Statistical Analysis and Display of Landing Sites; Automated Assignment of Proposals to Reviewers; Array-Pattern-Match Compiler for Opportunistic Data Analysis; Pre-Processor for Compression of Multispectral Image Data; Compressing Image Data While Limiting the Effects of Data Losses; Flight Operations Analysis Tool; Improvement in Visual Target Tracking for a Mobile Robot; Software for Simulating Air Traffic; Automated Vectorization of Decision-Based Algorithms; Grayscale Optical Correlator Workbench; "One-Stop Shopping" for Ocean Remote-Sensing and Model Data; State Analysis Database Tool; Generating CAHV and CAHVOmages with Shadows in ROAMS; Improving UDP/IP Transmission Without Increasing Congestion; FORTRAN Versions of Reformulated HFGMC Codes; Program for Editing Spacecraft Command Sequences; Flight-Tested Prototype of BEAM Software; Mission Scenario Development Workbench; Marsviewer; Tool for Analysis and Reduction of Scientific Data; ASPEN Version 3.0; Secure Display of Space-Exploration Images; Digital Front End for Wide-Band VLBI Science Receiver; Multifunctional Tanks for Spacecraft; Lightweight, Segmented, Mostly Silicon Telescope Mirror; Assistant for Analyzing Tropical-Rain-Mapping Radar Data; and Anion-Intercalating Cathodes for High-Energy- Density Cells.

Source record↗

Integration of in silico approaches to determination of endocrine-disrupting perfluorinated chemicals binding potency with steroidogenic acute regulatory protein

A myriad of perfluorinated compounds (PFCs) have the ability to interfere with steroidogenic acute regulatory (StAR) protein. Consequently, PFCs breaches cholesterol biotransformation in mitochondria and cause fatal consequences in steroidogenesis, however, these were poorly characterized. In the present study, we have evaluated toxic potencies, nuclear mediated probabilities and interaction profiles with StAR of PFCs using computational system biology tools. Toxicity endpoints revealed that PFCs contain high carcinogenicity, developmental toxicity, skin sensitization effects with low mutagenic activity. Consensus qualitative nuclear receptor agonist models show higher probability rates towards ER and PPAR-γ receptor than AR and AhR models were observed. To poise the subtle fluctuations of actual predictions, balanced accuracy and MCC were computed, and they signify perfect correlation ranges in all models. Screening studies resulting protein-ligand interaction profiles showed that residues Asn148, Asn150, Glu169, Ala171, Arg182, Phe184, Arg188, Trp241, Thr263 and Phe267 were identified as novel hotspots, participated in halogen bonds, H-bonds, atomic π-stacking, π-cation interactions and salt-bridges formation. Thus, the additional bonds contribute conformer stability that holds the protein structure at flexible state, so that PFCs acts as a barrier to cholesterol binding. From docking outcomes, representation space was created, that specifies high and medium StAR binders were occupied in toxic endpoints space with active concern. PFCs restrain molecular features and mitochondrial membrane disruption functions were revealed by efficient toxicogenomics studies. These data indicate toxicity and StAR protein binding levels of PFCs, sorted pinpoints could be useful in a promising way to know the other environmental pollutants and health risks. - Highlights: • In this study, QSAR models were revealed that PFCs have greater adverse toxicity along with nuclear receptors interaction potencies. • Binding potencies of PFCs against the StAR protein revealed only potential novel residue hotspots showed various bond patterns, and they sustain stability and complexity of StAR. • Through that, PFCs acts as a barrier in cholesterol binding and leads fatal consequences in steroidogenesis.

60 APPLIED LIFE SCIENCES↗

Magnetoresistance anomaly during the electrical triggering of a metal-insulator transition

Phase separation naturally occurs in a variety of magnetic materials and it often has a major impact on both electric and magnetotransport properties. In resistive switching systems, phase separation can be created on demand by inducing local switching, which provides an opportunity to tune the electronic and magnetic state of the device by applying voltage. Here we explore the magnetotransport properties in the ferromagnetic oxide La 0.7 ⁢Sr 0.3 ⁢MnO 3 (LSMO) during the electrical triggering of an intrinsic metal-insulator transition (MIT), which produces volatile resistive switching. This switching occurs in a characteristic spatial pattern, i.e., the formation of a high-resistance barrier perpendicular to the current flow, enabling an electrically actuated ferromagnetic-paramagnetic-ferromagnetic phase separation. At the threshold voltage of the MIT triggering, both anisotropic and colossal magnetoresistances exhibit anomalies including a large increase in magnitude and a sign flip. Computational analysis revealed that these anomalies originate from the coupling between the switching-induced phase separation state and the intrinsic magnetoresistance of LSMO. Furthermore, this work demonstrates that driving the MIT material into an out-of-equilibrium resistive switching state provides the means for electrical control of the magnetotransport phenomena.

Complex oxides↗

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗

Sonic Boom Prediction and Minimization of the Douglas Reference OPT5 Configuration

Conventional CFD methods and grids do not yield adequate resolution of the complex shock flow pattern generated by a real aircraft geometry. As a result, a unique grid topology and supersonic flow solver was developed at Northrop Grumman based on the characteristic behavior of supersonic wave patterns emanating from the aircraft. Using this approach, it was possible to compute flow fields with adequate resolution several body lengths below the aircraft. In this region, three-dimensional effects are diminished and conventional two-dimensional modified linear theory (MLT) can be applied to estimate ground pressure signatures or sonic booms. To accommodate real aircraft geometries and alleviate the burdensome grid generation task, an implicit marching multi-block, multi-grid finite-volume Euler code was developed as the basis for the sonic boom prediction methodology. The Thomas two-dimensional extrapolation method is built into the Euler code so that ground signatures can be obtained quickly and efficiently with minimum computational effort suitable to the aircraft design environment. The loudness levels of these signatures can then be determined using a NASA generated noise code. Since the Euler code is a three-dimensional flow field solver, the complete circumferential region below the aircraft is computed. The extrapolation of all this field data from a cylinder of constant radius leads to the definition of the entire boom corridor occurring directly below and off to the side of the aircraft's flight path yielding an estimate for the entire noise "annoyance" corridor in miles as well as its magnitude. An automated multidisciplinary sonic boom design optimization software system was developed during the latter part of HSR Phase 1. Using this system, it was found that sonic boom signatures could be reduced through optimization of a variety of geometric aircraft parameters. This system uses a gradient based nonlinear optimizer as the driver in conjunction with a computationally efficient Euler CFD solver (NIIM3DSB) for computing the three-dimensional near-field characteristics of the aircraft. The intent of the design system is to identify and optimize geometric design variables that have a beneficial impact on the ground sonic boom. The system uses a simple wave drag data format to specify the aircraft geometry. The geometry is internally enhanced and analytic methods are used to generate marching grids suitable for the multi-block Euler solver. The Thomas extrapolation method is integrated into this system, and hence, the aircraft's centerline ground sonic boom signature is also automatically computed for a specified cruise altitude and yields the parameters necessary to evaluate the design function. The entire design system has been automated since the gradient based optimization software requires many flow analyses in order to obtain the required sensitivity derivatives for each design variable in order to converge on an optimal solution. Hence, once the problem is defined which includes defining the objective function and geometric and aerodynamic constraints, the system will automatically regenerate the perturbed geometry, the necessary grids, the Euler solution, and finally the ground sonic boom signature at the request of the optimizer.

Siclari, Michael J.↗

3-D Reconstruction of Macular Type II Cell Innervation Patterns in Space-Flight and Control Rats

A semiautomated method for reconstructing objects from serial thin sections has been developed in the Biocomputation Center. The method is being used to completely, for the first time, type II hair cells and their innervations. The purposes are to learn more about the fundamental circuitry of the macula on Earth and to determine whether changes in connectivities occur under space flight conditions. Data captured directly from a transmission electron microscope via a video camera are sent to a graphics workstation. There, the digitized micrographs are mosaicked into sections and contours are traced, registered and displayed by semiautomated methods. Current reconstructions are of type II cells from the medial part of rat maculas collected in-flight on the Space Life Sciences-2 mission, 4.5 hrs post-flight, and from a ground control. Results show that typical type II cells receive processes from tip to six nearby calyces or afferents. Nearly all processes are elongated and have bouton-like enlargements; some have numerous vesicles. Multiple (2 to 4) processes from a single calyx to a type II cell are common, and approximately 1/3 of the processes innervale 2 or 3 type II cells or a neighboring cluster. From 2% to 6% of the cells resemble type I cells morphologically but have demi-calyces. Thus far, increments in synaptic number in type II cells of flight rats are prominent along processes that supply two hair cells. It is clear that reconstruction methods provide insights into details of macular circuitry not obtainable by other techniques. The results demonstrate a morphological basis for interactions between adjacent receptive fields through feed back-feed forward connections, and for dynamic alterations in receptive field range and activity during preprocessing of linear acceleratory information by the maculas. The reconstruction method we have developed will find further applications in the study of the details of neuronal architecture of more complex systems, to seek out shared organizational properties or neuronal networks and to understand better localization of synaptic changes in altered environments.

Ross, Muriel Dorothy↗

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Abstract Background Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors. Results In this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN. Conclusions DeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of Magmatic Activities on Early Mars Using Igneous Mineral Chemistry in Gale Crater, Mars

One objective of rover missions is exploring the geological context of the surroundings. Over the years, igneous petrology and sedimentology have been disconnected, the first investigating magmatic processes and volcanic activities, and the second seeking environmental conditions in the past and assessing the habitability of the planet. Although different, one is related to the other: igneous rocks are altered and broken down, leading to the formation of sedimentary rocks, which can in turn be used to back out the nature of their magmatic source. The Curiosity rover that landed in the 3.7 Gyr old impact crater Gale is traveling through sedimentary rocks. About fifty float rocks have been observed, and several of them with ambiguous texture and composition have been classified as igneous or sedimentary depending on studies such as Jake_M. The composition of several unambiguous igneous rocks has been analyzed [4- 6] but their heterogeneity at a larger instrumental (measurement size < 2 cm) scale prevents the measurement of a bulk composition as performed on Earth. An original approach avoiding these two last issues is to consider igneous mineral chemistry analyzed within igneous and sedimentary rocks to assess magmatic processes that could have formed them. Most Curiosity data are used to explore ancient environmental conditions, and a significant number of compositional analyses are under-explored for constraining magmatic activities. We will present how we can make use of sedimentary data for investigating igneous processes in the vicinity of Gale crater. Geological Context: We focus on the first 750 martian days, corresponding to measurements in a coherent lacustrine sedimentary unit called Bradbury, because all sedimentary rocks were sourced from the same watershed and appear to have a consistent source with minimal alteration [2-3]. Igneous detrital minerals including feldspar and pyroxene, are observed in sedimentary rocks. Monte Carlo models showed that minimal cation loss is observed based on the composition of all Bradbury rocks, implying negligible weathering [3]. Although clay minerals are detected in few rocks [7], chemical compositions of rocks can be explained by a mixture of primary igneous minerals [3]. Variation of composition within Bradbury rocks can be explained by mineral sorting and one distinct source component. While a common magmatic source is suggested, Bradbury sediments likely come from several volcanic eruptions from a single magmatic chamber [9- 10]. The occurrence of alkali minerals like sanidine and K-rich rocks throughout Bradbury supports the presence of a potassic component, likely trachytic, while plagioclase and a mafic composition suggest a basaltic component [8-9]. Instruments: Mineral chemistry can be estimated by three instruments onboard Curiosity. The CheMin instrument enables detection of mineral assemblages using X-ray diffraction (XRD). Using Rietveld refinement, each mineral is identified according to their 1D XRD pattern [11]. Note that distinction between pyroxene minerals is challenging with the CheMin instrument due to overlapping peaks on XRD patterns and low angular resolution of the instrument [12]. Then, using least square regression and optimization algorithms based on unit-cell parameters, mineral chemistry has been estimated by [11]. Plagioclase composition has been estimated using the NaAlSi3O8- CaAl2Si2O8 system and alkali feldspar is based on the NaAlSi3O8-KAlSi3O8 system (stars in Fig.1). Two mudstone samples (John Klein and Cumberland) and one sandstone sample (Windjana) were analyzed by CheMin at Yellowknife Bay and Kimberley, respectively. Figure 1. Ternary diagrams of feldspars (top) and pyroxene (bottom) quadrilateral. Stars correspond to CheMin composition and the gray patches to ChemCam composition. The colored dots are the composition of feldspar and pyroxene that crystallized during fractional crystallization at FMQ+1 of a melt extracted at distinct melting degree during the adiabatic ascent of a primitive mantle composition, without any water (left panels) and with 0.5 wt.% of water (right panels) at distinct pressure. The ChemCam instrument enables the analysis of the chemical compositions of rocks at hundreds of micrometer scale (350-550 μm) using laser induced breakdown spectroscopy (LIBS), which may provide the composition of minerals when they are larger than the beam spot (>550 μm) [13]. Within >5000 LIBS points, we performed a typical stoichiometric filtering allowing us to distinguish 56 feldspar and 10 pyroxene mineral compositions (grey patches in Fig. 1). Finally, the Alpha Particle X-ray Spectrometer (APXS) analyzes the composition of rocks with a 1.6 cm diameter spot size. Monte Carlo mass balance modeling allowed [3] to decipher a feldspar range varying between An30 and An40 (Fig. 1). Discussion: Although there could be a more complex history and other ways to form the whole compositional range of igneous minerals analyzed within the Bradbury formation, we are presenting here simple magmatic pathways commonly occurring on Earth using the thermodynamical softwares pMELTS and rhyoliteMELTS [14]. The objective is to find reasonable igneous processes that produce minerals that parallel the compositions of feldspar and pyroxene analyzed by the Curiosity rover. As commonly observed for mid-ocean ridge basalts, the adiabatic ascent of a primitive mantle composition [15] partially melting at 2 GPa has been modeled, followed by the extraction of a liquid at distinct degrees of partial melting, which undergoes fractional crystallization at an oxygen fugacity +1 log unit above the fayalite-magnetite-quartz (FMQ) buffer within the crust (0.02-0.4 GPa) with H2O = 0- 0.5 wt. %. These latter conditions correspond to those recorded within igneous clasts from the Noachian martian breccia NWA 7034 and paired and within Gale igneous rocks (colored dots in Fig. 1) [16-17]. To check the reliability of these 2-step models, we also tested fractional crystallization at similar conditions (FMQ+1; P=0.02-0.4 GPa; H2O = 0-0.5 wt. %) of starting compositions corresponding to that of magmas with distinct melting degrees obtained from isobaric experiments at 2 GPa [18]. Mineral compositions obtained from both models are similar. As shown on Fig. 1, the whole range of observed feldspar compositions cannot be reproduced by fractionation of one magma only. Indeed, while alkali feldspar and Na-plagioclase likely crystallized from fractional crystallization of a low-degree melt (here <15%), plagioclase and pyroxene can only be formed by fractional crystallization of a higher degree melt (here >19%). The corresponding liquid descent lines are broadly in agreement with compositions estimated by ChemCam corresponding to float igneous rocks (Fig. 2) [4-6]. Figure 2. Silica versus alkali content. Lines show the liquid lines of descent from magmas with distinct degrees of melting. Gray patches represents the composition of Gale igneous rocks [4-6]. Trachytic to rhyolitic magmas crystallize alkali feldspar, and andesite to dacite magmas likely form plagioclase. Therefore, at least two starting magmas at distinct melting degrees, which could easily come from a single mantle source, are necessary to explain the whole compositional range of feldspar and pyroxene analyzed within Bradbury rocks. Conclusion: Because rocks from the Bradbury formation are likely originating from the same magmatic source with minimal weathering as supported by several studies using different approaches, igneous mineral chemistry analyzed by CheMin and ChemCam allows us to back out reasonable magmatic pathways that could have crystallized them. Fractional crystallization of at least two starting magmas originating from distinct melting degrees of a single mantle source can explain the whole range of feldspar and pyroxene composition. Both alkaline and sub-alkaline liquids can be produced, with compositions corresponding to those of the igneous rocks analyzed by ChemCam within the Bradbury formation, highlighting the complexity of Mars magmatism.

Payre, V.↗

Nanotube/Quantum Dot-Polymer Solar Cells

Single wall carbon nanotubes used or this study were synthesized using the pulse laser vaporization technique. The as-produced SWNTs were collected from the condensed region on the quartz tube outside the furnace and purified by modification of the previously reported procedure. Preparation of the SWNT-P3OT composite solutions was performed using a series of mixing and sonication steps as previously demonstrated for other SWNT-polymer systems. Device fabrication involved the use of commercially-obtained, high quality (i.e., less than 10 W/sq.) ITO-coated polyethylene terapthalate (PET) substrates. Initially, an intrinsic layer of pristine P3OT is spray deposited (approx. 1-2 mL of the 15 mg/mL solution) onto the masked, 1 sq in. active area of the substrate. This is followed with spray deposition of the SWNT-P3OT composite solutions at similar volumes. As seen completion of the solar cell occurs when aluminum contacts (typical thicknesses of l000A) are applied to the IT0 and SWNT-P3OT composite film layers. The homogeneous distribution of SWNTs in a polymer matrix is dependent upon the ability of the polymer chain to associate with the SWNT superstructure. Stable composite dispersions of 0.1 % and 1.0% w/w SWNTs in P3OT were produced and analyzed in this study. Optical spectroscopy was conducted to observe the SWNT doping level effects on the absorption properties and infer potential electronic interactions between dopant and polymer. Shown is an overlay of these spectra where the pristine P3OT shows strong optical absorption at energies less than 2 eV. As expected, variation in absorption properties for the SWNT-P3OT composites is observed as the doping level increases. Through modification of the SWNT doping level in the polymer, it is possible to alter the absorption pattern of these composite materials. In fact, at these relatively low doping levels, the P3OT shows a significant enhancement in absorption through the near-IR and visible regions. The gray curve for purified SWNTs is offset from the other three for clarity, but indicates the typical complex pattern observed for this spectral range.

Bailey, Sheila G.↗