Modeling microbial community structure and functional diversity across time and space
Abstract not provided
GILBERT, J G↗
SEARCH · Engineering Papers
Results for “STRUCTURAL MODELS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Coarse graining approach to First principles modeling of structural materials
Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an e cient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the rst principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force eld. The local moments in the neighborhood of the defect cores are calculated with rst-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs signi cantly and makes large-scale structures amenable to rst principles study. Work is sponsored by the USDoE, O ce of Basic Energy Sciences, Center for Defect Physics, an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the O ce of Science of the USDoE under Contract No. DE-AC05-00OR22725.
coarse grained↗
Structural Analysis and Performance-Based Validation of a Composite Wing Spar
Electric-motor powered aircraft possess the ability to operate with efficient energy delivery, but lack the operational range of internal combustion engine powered aircraft. This range limitation requires the use of high aspect ratio, thin-chord wings to minimize aerodynamic drag losses, which results in highly loaded composite spar structures. High aspect ratio wings are required to increase mission durations for a NASA-developed experimental multi-rotor electric powered aircraft denoted as the Scalable Convergent Electric Propulsion Technology and Operations Research (SCEPTOR) or “X-57”. This paper examines the structural performance of the composite main wing spars to validate spar strength using ply-based laminate finite element methods. Geometric scaling of a main spar test-section was initially proposed for proof-testing but sacrificed stability. Ply-based structures modeling with local structural features was implemented as a risk-reduction methodology. Ply-based modeling was selected to augment the conventional “building block” approach to reduce risk, and leverage a “performance-based” approval processes encouraged in Federal Aviation Administration (FAA) design guidance. Therefore, ply-based laminate modeling of the full-scale main spar and forward spar shear-web attachments were subsequently undertaken to determine load path complexity with predicted flight loads. Ply-based modeling included stress concentrations and interlaminate behavior at interface locations that can be obscured in traditional finite element sizing models. Analysis of the wing spar laminate ply-based models compared with bearing test coupon performance was used to reduce future wing assembly proof-testing burden and facilitate performance-based flight hardware safety for the X-57 experimental aircraft.
Moore, James B.↗
Mapping the three-dimensional “x-shaped structure” in models of the Galactic bulge
Numerical simulations have shown that the X-shaped structure in the Milky Way bulge can naturally arise from bar instability and buckling instability. To understand the influence of buckling amplitude on the morphology of the X-shape, we analyze three self-consistent numerical simulations of barred galaxies with different buckling amplitudes (strong, intermediate, and weak). We derive the three-dimensional density using an adaptive kernel smoothing technique. The face-on isodensity surfaces are all elliptical, while in the edge-on view, the morphology of buckled bars transitions with increasing radius from a central boxy core to a peanut bulge and then to an extended, thin bar. Based on these isodensity surfaces at different density levels, we find no clear evidence for a well-defined structure shaped like the letter X. The X-shaped structure is more peanut-like, the visual perception of which is probably enhanced by the pinched inner concave isodensity contours. The peanut bulge can reproduce qualitatively the observed bimodal distributions that were used as evidence for the discovery of the X-shape. The central boxy core is shaped like an oblong tablet, extending ∼500 pc above and below the Galactic plane (|b|∼4{sup ∘}). From the solar perspective, lines of sight passing through the central boxy core do not show bimodal distributions. This generally agrees with the observations that double peaks merge at |b| ∼ 4°–5° from the Galactic plane, indicating the presence of a possibly similar structure in the Galactic bulge.
79 ASTRONOMY AND ASTROPHYSICS↗
Oxygen Defect Configurations in Single-Phase UO 2.15
Hyperstoichiometric UO 2.15 was characterized by neutron total scattering at high temperature in the single-phase UO 2+x region of the U/O phase diagram. The diffraction data confirmed a single-phase fluorite structure at high temperature. Analysis of the short-range data showed that the same structural model does not fit the pair distribution functions well. Instead, structural models containing specific configurations of oxygen defect clusters best represent the local atomic arrangement. In conclusion, prevalent defect clusters previously proposed were fit to the experimental data, and moderately distorted oxygen cuboctahedra hypothesized by recent molecular dynamics simulations fit the data most accurately.
neutron pair-distribution function analysis↗
Using in situ X-ray absorption spectroscopy to study the local structure and oxygen ion conduction mechanism in (La{sub 0.6}Sr{sub 0.4})(Co{sub 0.2}Fe{sub 0.8})O{sub 3-{delta}}
To study the local structure and oxygen ion conduction mechanism in (La{sub 0.6}Sr{sub 0.4})(Co{sub 0.2}Fe{sub 0.8})O{sub 3-{delta}} (LSCF) as a function of the oxygen partial pressure (P(O{sub 2})), in situ the Co and Fe K-edge X-ray absorption spectroscopy (XAS) was measured at elevated temperatures of 900 and 1000 K. The reduction of the Co and Fe valence, i.e., the oxygen content (3-{delta}) in LSCF, followed the change of P(O{sub 2}) from 1 to 10{sup -4} atm during{approx}4000 s. The quantitative analysis of the X-ray absorption near edge structure (XANES) and the extended X-ray absorption fine structure (EXAFS) indicated that the Fe valence was higher than the Co valence at oxidative condition ({delta} Almost-Equal-To 0) in LSCF. Whereas the Co valence decreased more than the Fe valence after reduction of P(O{sub 2}) at both 900 and 1000 K. From the relaxation plots of the valence and the oxygen content (3-{delta}) for Co and Fe after changing P(O{sub 2}), we successfully determined D{sub chem} and E{sub a} of an oxygen ion migration around Co and Fe in LSCF. A structural model with and without oxygen vacancies and an oxygen ion conduction mechanism for LSCF are proposed based on these results. - Graphical abstract: A structural model with and without oxygen vacancies, and the oxygen ion conduction mechanism of LSCF were speculated. In other words, oxygen vacancies would form more preferentially around Co than Fe from the results of in situ XAS analysis during reduction, and oxygen ions needs to pass through at the vicinity of Fe from the results of D{sub chem} and E{sub a}. Highlights: Black-Right-Pointing-Pointer Study of the oxygen ion conduction mechanism in (La{sub 0.6}Sr{sub 0.4})(Co{sub 0.2}Fe{sub 0.8})O{sub 3-{delta}} (LSCF). Black-Right-Pointing-Pointer Using in situ X-ray absorption for study of valence and oxygen diffusion coefficient. Black-Right-Pointing-Pointer The oxygen vacancies should be preferentially localized around Co in LSCF. Black-Right-Pointing-Pointer The values of the dynamics parameters for Co and Fe are close to each other.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High throughput, accurate gene annotation through AI and HPC-enabled structural analysis
With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.
59 BASIC BIOLOGICAL SCIENCES↗
Sources of Uncertainty in Predicting Land Surface Fluxes Using Diverse Data and Models
In the domain of predicting land surface fluxes, models are used to bring data from large observation networks and satellite remote sensing together to make predictions about present and future states of the Earth. Characterizing the uncertainty about such predictions is a complex process and one that is not yet fully understood. Uncertainty exists about initialization, measurement and interpolation of input variables; model parameters; model structure; and mixed spatial and temporal supports. Multiple models or structures often exist to describe the same processes. Uncertainty about structure is currently addressed by running an ensemble of different models and examining the distribution of model outputs. To illustrate structural uncertainty, a multi-model ensemble experiment we have been conducting using the Terrestrial Observation and Prediction System (TOPS) will be discussed. TOPS uses public versions of process-based ecosystem models that use satellite-derived inputs along with surface climate data and land surface characterization to produce predictions of ecosystem fluxes including gross and net primary production and net ecosystem exchange. Using the TOPS framework, we have explored the uncertainty arising from the application of models with different assumptions, structures, parameters, and variable definitions. With a small number of models, this only begins to capture the range of possible spatial fields of ecosystem fluxes. Few attempts have been made to systematically address the components of uncertainty in such a framework. We discuss the characterization of uncertainty for this approach including both quantifiable and poorly known aspects.
Dungan, Jennifer L.↗
Space Infrared Telescope Facility/Multimission Modular Spacecraft Attitude Control System conceptual design
A control system utilizing the Multi-mission Modular Spacecraft (MMS) Attitude Control System (ACS) was developed and analyzed for the Space Infrared Telescope Facility (SIRTF) spacecraft. Alternative torquer augmentation schemes were studied to determine viable ACS approaches. A control law was developed to use a dual set of single-axis Control Moment Gyros (CMGs) for two-axis control. Flexible structural models were developed using a high fidelity, flight tested NASTRAN model of the MMS, coupled with a NASTRAN model of the SIRTF telescope. Modal significance criteria were employed to reduce the structural model. Multivariable interactive techniques were used to synthesize the control system (including the structural filters). Control system performance for the SIRTF operational modes (quiescent inertial hold, slewing, nodding, and rastering) was then determined using both single-axis and three-axis simulations). The control system described met performance requirements for all modes but the raster with the use of CMGs. The raster performance was limited by the structural flexibility.
Class, Brian F.↗
The Impact of Model and Rainfall Forcing Errors on Characterizing Soil Moisture Uncertainty in Land Surface Modeling
The contribution of rainfall forcing errors relative to model (structural and parameter) uncertainty in the prediction of soil moisture is investigated by integrating the NASA Catchment Land Surface Model (CLSM), forced with hydro-meteorological data, in the Oklahoma region. Rainfall-forcing uncertainty is introduced using a stochastic error model that generates ensemble rainfall fields from satellite rainfall products. The ensemble satellite rain fields are propagated through CLSM to produce soil moisture ensembles. Errors in CLSM are modeled with two different approaches: either by perturbing model parameters (representing model parameter uncertainty) or by adding randomly generated noise (representing model structure and parameter uncertainty) to the model prognostic variables. Our findings highlight that the method currently used in the NASA GEOS-5 Land Data Assimilation System to perturb CLSM variables poorly describes the uncertainty in the predicted soil moisture, even when combined with rainfall model perturbations. On the other hand, by adding model parameter perturbations to rainfall forcing perturbations, a better characterization of uncertainty in soil moisture simulations is observed. Specifically, an analysis of the rank histograms shows that the most consistent ensemble of soil moisture is obtained by combining rainfall and model parameter perturbations. When rainfall forcing and model prognostic perturbations are added, the rank histogram shows a U-shape at the domain average scale, which corresponds to a lack of variability in the forecast ensemble. The more accurate estimation of the soil moisture prediction uncertainty obtained by combining rainfall and parameter perturbations is encouraging for the application of this approach in ensemble data assimilation systems.
Maggioni, V.↗
A finite element-analytical method for modeling a structure in an infinite fluid
A method is described from which the interaction of an elastic structure with an infinite acoustic fluid is determined. The displacements of the structure and the pressure field of the immediate surrounding fluid are modeled by finite elements, and the remaining pressure field of the infinite fluid region is given by an analytical expression. This method yields a frequency dependent boundary condition for the outer fluid boundary when applied to the frequency response of an elastic beam in contact with an acoustic fluid. The frequency response of the beam is determined using NASTRAN, and compares favorably to the exact solution which is also presented. The effect of the fluid on the response of the structure at low and high frequencies is due to added mass and damping characteristics, respectively.
Zarda, P. R.↗
Surface termination structure of α-Ga{sub 2}O{sub 3} film grown by mist chemical vapor deposition
The surface structure of α-Ga{sub 2}O{sub 3}(0001) grown on an α-Al{sub 2}O{sub 3}(0001) substrate by mist chemical vapor deposition was studied by coaxial impact-collision ion scattering spectroscopy (CAICISS) and atomic force microscopy (AFM). The minimum step height observed in the AFM image was 0.21 ± 0.01 nm, coinciding with the height of three atomic layers of α-Ga{sub 2}O{sub 3}(0001). It was revealed by CAICISS analysis that the surface of α-Ga{sub 2}O{sub 3}(0001) is terminated by a Ga layer followed by an O layer, which is consistent with the surface termination of α-Al{sub 2}O{sub 3}(0001). A structural model taking surface relaxation into account was also constructed by fitting the simulated curve for the azimuth angle dependence of the Ga intensity to the experimental dependence. The resultant structural model is similar to the model of an α-Al{sub 2}O{sub 3}(0001) surface, which indicates analogous behavior in corundum crystals.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
The Dependence of ITCZ Structure on Model Resolution and Dynamical Core in Aquaplanet Simulations
Aqua-planet simulations using the Community Atmosphere Model version 4 (CAM4) with the Model for Prediction Across Scales Atmosphere (MPAS-A) and Higher Order Method Modeling Environment (HOMME) dynamical cores and zonally symmetric sea surface temperature (SST) structure are studied to understand the dependence of the inter-tropical convergence zone (ITCZ) structure on resolution and dynamical core. While all resolutions in HOMME and the low-resolution MPAS-A simulations give a single equatorial peak in zonal mean precipitation, the high-resolution MPAS-A simulations give a double ITCZ with precipitation peaking around 2° to 3° on either side of the equator. This study reveals that the structure of ITCZ is dependent on the feedbacks among convection and large-scale circulation and surface heat fluxes. We show that, by increasing convective available potential energy (CAPE) off the equator, the simulations with higher wind induced surface heat fluxes result in double ITCZ structure. This in turn leads to stronger convection and positive feedback with the large-scale circulation. We further show that the dominance of anti-symmetric waves in a model is not enough to cause double ITCZ, and the lateral extent of equatorial waves does not play an important role in determining the width of the ITCZ but rather the latter may influence the former.
aqua-planet↗
The Use of Raman Spectroscopy and Methods of Quantum Chemistry for Assessing the Relative Concentration of Triglycerides of Oleic and Linoleic Acids in a Mixture of Olive Oil and Sunflower Seed Oil
The Raman spectra of five samples of sunflower seed oil and five samples of cold-pressed olive oil of various brands are recorded in the range of 500–2000 cm{sup –1}. Within the framework of the B3LYP/6-31G(d)/6-31G(d,p)/6-31+G(d,p)/6-311G(d)/6-311G(d, p)/6-311+G(d,p) methods, the structural models of eight fatty acids (oleic, linoleic, palmitic, stearic, α-linolenic, arachidonic, eicosapentaenoic, and docosahexaenoic) are constructed, and also within the framework of the B3LYP/6-31G(d) method, the structural models of triglycerides of the first four of the above acids are obtained. The vibrational wavenumbers and intensities in the IR and Raman spectra are calculated. The Raman spectra of olive oil and sunflower seed oil were simulated by using the supermolecular approach. We investigated the dependence of the relative intensity of the vibrational bands ν{sub exp} = 1660 and 1445 cm{sup –1} on the concentration of triglycerides in oils of oleic and linoleic acids and the dependence of the intensity of these bands on the degree of saturation of fatty acids. Experimental and empirical dependences are constructed to estimate the relative concentration of triglycerides of oleic and linoleic acids in a mixture of olive oil and sunflower seed oil. The applicability of the density functional theory together with the vibrational spectroscopy for the identification of mixtures of vegetable oils is discussed.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Unified Theory for Aircraft Handling Qualities and Adverse Aircraft-Pilot Coupling
A unified theory for aircraft handling qualities and adverse aircraft-pilot coupling or pilot-induced oscillations is introduced. The theory is based on a structural model of the human pilot. A methodology is presented for the prediction of (1) handling qualities levels; (2) pilot-induced oscillation rating levels; and (3) a frequency range in which pilot-induced oscillations are likely to occur. Although the dynamics of the force-feel system of the cockpit inceptor is included, the methodology will not account for effects attributable to control sensitivity and is limited to single-axis tasks and, at present, to linear vehicle models. The theory is derived from the feedback topology of the structural model and an examination of flight test results for 32 aircraft configurations simulated by the U.S. Air Force/CALSPAN NT-33A and Total In-Flight Simulator variable stability aircraft. An extension to nonlinear vehicle dynamics such as that encountered with actuator saturation is discussed.
Hess, R. A.↗
A Review on Lignin Liquefaction: Advanced Characterization of Structure and Microkinetic Modeling
Lignin liquefaction microkinetics is a move toward a more first principles (i.e., ab initio) based understanding at the molecular level in reaction engineering. While the microkinetic modelling of reactions to obtain kinetic rate parameters of chemical reactions have been widely used in the field of gas phase combustion and heterogeneous catalysis, this approach has not been as thoroughly developed in the area of biomass thermochemical reactions (e.g., lignin pyrolysis, hydrothermal liquefaction). The difficulties in establishing the structure of complex heterogeneous materials, like lignin, is perhaps the main challenge in developing rational microkinetic descriptions of biomass thermochemical reactions. In this manuscript we review the current state of the art and the challenges to develop microkinetic models for lignin liquefaction technologies (e.g., pyrolysis, hydrothermal liquefaction, solvolysis). A general strategy for the development of microkinetic models for lignin liquefaction technologies is discussed. Here, the first hurdle is to obtain sufficiently rich experimental data of lignin underlying polymeric structure and methodologies to use this data to build realistic lignin structural representations. Some analytical techniques for lignin structural characterization and their associated data, as well as a correlation for calculating the degree of macromolecular lignin branching are discussed. The presence of small lignin oligomeric structures and the role of these structures in lignin pyrolysis is also addressed. The ways in which elementary deconstruction and repolymerization reactions occur within this structure to form a liquid intermediate, and how these deconstruction products continue to interact with each other until they are removed from the liquid intermediate is thoroughly discussed. Further, experimental work with model compounds and the effect of reaction parameters (e.g., temperature, pressure, vapor residence time) are reviewed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Thermoviscoplastic response of thin plates subjected to intense local heating
A finite element method is employed to investigate the thermoviscoplastic response of a half-cylinder to intense localized transient heating. Thermoviscoplastic material behavior is characterized by the Bodner-Partom constitutive model. Structure geometry is modeled with a three-dimensional assembly of CST-DKT plate elements incorporating the large deflection von Karman assumptions. The paper compares the results of a dynamic analysis with a quasi-static analysis for the half-cylinder structure with a step-function transient temperature loading similar to that which may be encountered with shock wave interference on a hypersonic leading edge.
Byrom, Ted G.↗
Automation of Structural Sizing of Aircraft Concepts Under Static Aeroelastic Constraints
This paper presents an automation process for structural sizing of subsonic and supersonic aircraft concepts under static aeroelastic constraints. The automation process starts with an OpenVSP geometry and ends with a PATRAN plot of a NASTRAN solution for static aeroelastic analysis or optimization. ModelCenter is used to integrate all analysis codes with easy-to-use interfaces. Automation tools are developed to streamline the setup process and avoid user errors. Fuel is distributed by solving an optimization problem to match the center of gravity of aircraft at a specified flight condition. Fuel weights are also automatically attached to the structural model as point masses. All other weights used in FLOPS mission analysis (excluding fuselage and wing structural weights) are automatically attached to or smeared on the structural model. For any given OpenVSP geometry and FLOPS analysis data, a static aeroelastic sizing model for NASTRAN analysis can be generated in a couple of hours. The empirical fuselage and wing structural weights from FLOPS are replaced by structural panel weights from the sized finite-element model. Three supersonic and two subsonic aircraft concepts are used to demonstrate the automation process as a physics-based weight estimation tool for aircraft conceptual design.
Li, Wu↗