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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Medium amplitude parallel superposition (MAPS) rheology. Part 2: Experimental protocols and data analysis

An experimental protocol is developed to directly measure the new material functions revealed by medium amplitude parallel superposition (MAPS) rheology. This protocol measures the medium amplitude response of a material to a simple shear deformation composed of three sine waves at different frequencies, revealing a rich dataset consisting of up to 19 measurements of the third-order complex modulus at distinct three-frequency coordinates. We discuss how the choice of input frequencies influences the features of the MAPS domain studied by the experiment. A polynomial interpolation method for reducing the bias of measured values from spectral leakage and reducing variance due to noise is discussed, including a derivation of the optimal range of amplitudes for the input signal. This leads to the conclusion that conducting the experiment in a stress-controlled fashion possesses a distinct advantage to the strain-controlled mode. The experimental protocol is demonstrated through measurements of the MAPS response of a model complex fluid: a surfactant solution of wormlike micelles. The resulting dataset is indeed large and feature-rich, while still acquired in a time comparable to similar medium amplitude oscillatory shear (MAOS) experiments. We demonstrate that the data represent measurements of an intrinsic material function by studying its internal consistency, compatibility with low-frequency predictions for Coleman–Noll simple fluids, and agreement with data obtained via MAOS amplitude sweeps. Finally, the data are compared to predictions from the corotational Maxwell model to demonstrate the power of MAPS rheology in determining whether a constitutive model is consistent with a material’s time-dependent response.

Lennon, Kyle R. (ORCID:0000000212515461)↗
DOE OSTI2019

Deformation Behavior and Microstructure Evolution of Powder Metallurgy Ti6Al4V Alloy During Hot Compression

In order to determine appropriate workability parameters for cross-wedge rolling products of powder metallurgy (PM) Ti6Al4V alloys, thermal compression experiments were carried out within the temperature range of 850-1050 °C, the strain rate range of 0.1-10 s{sup −1}, and with a height decrease of 60%. The compression deformation behavior was investigated. A strain-compensated constitutive model was established based on the flow stress curves corrected by the friction, which can predict the flow behaviors under the entirety of the experimental deformation conditions. Moreover, the processing map was developed, and stable and unstable deformation regimes were established. The microstructure analysis illustrated that globularization and dynamic recrystallization were the main deformation mechanisms. The porosity of the compressed samples was greatly reduced and influenced by the temperature and strain rate. Considering the material flow stress, hot processing map, microstructure and porosity, the appropriate hot deformation parameters for PM Ti6Al4V alloy preforms are suggested.

36 MATERIALS SCIENCE↗
DOE OSTI2019

A Comparative Study of Constitutive Characteristics and Microstructure Evolution between Uniaxial and Plane Strain Compression of an AA6061 Alloy

The hot deformation behavior of an AA6061 alloy was comparatively studied by uniaxial compression (UC) and plane strain compression (PSC) in the temperature range of 300-450 °C and strain rate range of 0.01-5 s{sup −1}. The processing maps were constructed based on a dynamic materials model, and the associated microstructures were observed. Under the same deformation conditions, the flow stress of the AA6061 alloy during PSC is higher than that during UC, which can be characterized by the Zener–Hollomon (Z) parameter in a hyperbolic sine-type equation with an activation energy Q of 175.2 kJ mol{sup −1} and 201.9 kJ mol{sup −1}, respectively. In addition, the instability domain is narrower under PSC compared to that under UC. The observed microstructures also indicate that as the Z value decreases, the tendency of dynamic recrystallization increases during PSC. The softening mechanisms in the AA6061 alloy after PSC and UC mainly consist of the dynamic recovery that is accompanied by a slight dynamic recrystallization. The optimum parameters are in the temperature range of 360-450 °C and strain rate range of 0.03-0.3 s{sup −1} for UC, and for PSC, the optimum parameters are in the temperature range of 320-400 °C and strain rate range of 0.01-0.05 s{sup −1}.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Interpreting the Strain Tensor During Injection into a Reservoir

A suite of well tests was conducted to evaluate the feasibility of measuring and interpreting the strain tensor during injection. Water was injected at 1 liter/s for a few days to a few weeks into a well completed at a depth of 530 m in the Bartlesville sandstone in the North Avant Field in Oklahoma. The strain tensor was measured using strainmeters at a depth of 30m and a distance of 220m from the well. We used a Gladwin strainmeter, a state-of-the-art geodetic strainmeter, as well as novel borehole strainmeters developed for the project. After processing, the horizontal strains were tensile and the vertical strain was compressive during injection. The radial strain was less than the circumferential strain. Strain magnitudes increased during injection and recovered afterward. The strain rate was as fast as 100 nanostrain/d at the start of injection, and decreased to 10 nanostrain/d after a few days. The normal strain signals were approximately proportional to the log of time during the first few days of injection, and the semi-log slope was 50 to 75 nanostrain. Data from the Gladwin strainmeter were essentially identical to data from a strainmeter we developed using optical fiber sensors. Tilt was measured using two tiltmeters, but the tilts were erratic compared to the normal strain and were of limited value. Strain data were analyzed using a strain type-curve method, an analytical solution to a poroelastic inhomogeneity, and a stochastic inversion method. Poroelastic simulations explain the data well. Results from the interpretation methods are consistent with each other, and with independent information characterizing the area. The hydraulic diffusivity is approximately 0.5 m2/s and the permeability is between 100 and 500 mD, according to analysis of the strain signals. This is consistent with measurements of permeability from cores, and with analyses of pressure transients. The analyses indicate that Young’s modulus of the reservoir is between 2 and 6 GPa. Strain interpretations indicate the well intersects a permeable lens with a maximum dimension of 500 to 1,000 m. An isopach map of coarse-grained sand confirms a feature roughly 1,000 m in lateral extent. The results demonstrate that the strain signal measured at shallow (30m) depth can be used to infer properties and heterogeneities in an underlying reservoir or aquifer.

Murdoch, Larry↗
DOE OSTI2024

Stress Relaxation Cracking in 347H Stainless Steel Arc Welds: Susceptibility Evaluation of Heat-Affected Zone

Stress relaxation cracking (SRC) is considered one of the major failure mechanisms for 347H stainless steel welds at elevated service temperatures or during post weld heat treatment (PWHT), especially within the heat-affected zone (HAZ). This work focuses on the characterization of SRC susceptibility within 347H physically simulated arc welded HAZ at elevated temperatures. A four-step SRC thermomechanical test in combination with finite element modeling (FEM) of the welding and testing processes is developed to establish a susceptibility map for HAZ. The test first runs a thermal cycle with three different peak temperatures (1335, 1275, and 1150 °C) to duplicate representative HAZ subzone microstructures, followed by time-to-failure examination under a variety of pre-stress (260–600 MPa) and pre-strain conditions (0.03–0.19) as a function of reheat temperatures between 750 and 1050 °C. With the aid of FEM, SRC susceptibility maps are generated to identify the threshold stress, plastic strain, and creep strain as a function of test temperature. It was found out that HAZ subzone with a lower peak temperature (1150 °C) appears to be slightly less susceptible to SRC than the other two subzones that experienced higher peak temperatures. Generally, time-to-fracture reduces with increasing initially applied stress and strain for all test temperatures. The pre-stress thresholds decrease from about 500 to 330 MPa as the testing temperature increases from 800 to 1050 °C, while the corresponding initial plastic strain thresholds reduces from 0.15 to 0.06. The SRC susceptibility was also evaluated through the Larson–Miller Parameter (LMP) analysis as a function of plastic strain, initial stress and starting stress upon reaching the testing temperature, respectively. The 1050 °C test with a high pre-applied strain (0.1) exhibits an extremely short time to failure (t = 3 s) that lies outside the general trend in LMP analysis. Additionally, it was identified that a plastic strain above 0.07 is identified to significantly reduce the bulk creep strain tolerance to fracture and therefore increases SRC susceptibility. Hardness measurement and fractography analysis indicated that the strain aging of niobium carbonitrides and other potential phases in conjunction with intergranular precipitates contributes to an increase in microhardness and increased intergranular cracking susceptibility.

14 SOLAR ENERGY↗
DOE OSTI2020

Hydrostatic pressure mapping of barium titanate phase transitions with quenched FeRh

We report a pressure study of the metamagnetic/ferroelectric hybrid heterostructure of a quenched FeRh thin film (25nm) grown on single crystal barium titanate (BTO). It has been previously reported that when the BTO undergoes a crystal transition a massive magnetization and coercivity change is triggered in the highly strain sensitive quenched FeRh thin film. Therefore quenched FeRh makes for an ideal probe for mapping a materials structural phase transitions. In this work we demonstrate this effect as a function of both temperature and hydrostatic pressure. As a result, we present the pressure dependence of the hybrid material which aligns identically with the BTO substrates pressure dependence reported in literature. The concept of combining a structural phase transitional (SPT) material with a magnetostrictive magnetic metal has been shown with vanadium oxides and our findings here prove that this methodology can be extended to strain sensitive metamagnetic materials systems in thin film, and possibly in bulk, heterostructures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Primal interface debonding formulation for finite strain isotropic plasticity

In this work, a framework is developed for modeling ductile damage of nonlinear materials whose plastic deformation is characterized using rate independent classical plasticity. This method relies on the assumption that the free energy can be decomposed into elastic, plastic and damage parts. A thermodynamically consistent method is derived which satisfies the second law of thermodynamics in the Clausius–Duhem inequality form. The dissipation associated with plasticity takes place in the domain only, while damage dissipation is localized to the interface. The method is developed using Variational Multiscale ideas to obtain definitions of the interface fluxes within a primal formulation analogous to the Discontinuous Galerkin method, which ensures weakly vanishing interface gap prior to reaching a damage initiation criterion. The local nonlinear problem to calculate both plastic deformation gradient and damage variable follows an incremental approach similar to classical plasticity return mapping algorithm. This elastoplastic damage formulation is developed for material undergoing finite strain, and it naturally accommodates a trapezoidal traction separation law (TSL) whose shape can be varied to model either ductile interface behavior or brittle interface behavior. The formulation's performance is assessed through modeling a patch test and a compact tension specimen.

42 ENGINEERING↗
DOE OSTI2025

Bulk segregant and QTL analysis of maltose metabolism in Saccharomyces eubayanus

This study investigates natural variation in maltose utilization among Saccharomyces eubayanus strains isolated from different tree hosts. An F2 population was generated from a cross between strain QC18 (Quercus-associated) and strain CL467.1 (Nothofagus-associated). Bulk segregant analysis (BSA) was performed on the F2 offspring, and QTL mapping was conducted by whole-genome sequencing of two pools of 30 segregants each, representing the lowest and highest growth in high maltose concentrations. For QTL analysis, the parental strains QC18 and CL467.1 were also sequenced.

evolutionary plasticity↗
DOE OSTI2021

In-Situ SEM High Strain Rate Testing of Large Diameter Micropillars Followed by TEM and EBSD Postmortem Analysis

Background Dislocation dynamic simulations are intended as a tool to understand and predict the mechanical behavior of metallic materials, but its prediction has never been directly verified by experiments due to differences in specimen strain rate and size. Objective In this work, a comprehensive experimental framework is proposed to attempt direct comparison between experiments and discrete dislocation dynamics (DDD) modelling. Methods By integrating high-throughput sample fabrication and a customized testing apparatus, the sample size and strain rate typically employed in DDD simulations are explored experimentally. Constitutive properties such as stress-strain response are measured, and microstructural information is obtained from transmission electron microscopy (TEM) imaging, electron backscatter diffraction (EBSD), and TEM-based orientation mapping. Results Magnesium and copper were selected, as case studies, to demonstrate the newly developed experimental procedure. Measured stress-strain responses for Mg are consistent with those obtained with a miniaturized Hopkison bar experiments. Furthermore, by exploiting the validated workflow, the effect of strain rate on micropillar heterogeneous deformation and associated dislocation plasticity were revealed. Conclusion The work establishes a methodology for the systematic study of not only metals but also other materials and structures at the microscale and high strain rates.

42 ENGINEERING↗
DOE OSTI2022

Identifying the gluc-1 and gluc-2 mutations in Neurospora crassa by genome resequencing

Genome resequencing is an efficient strategy for associating mutant phenotypes with physical genomic loci. A pilot study of this approach demonstrated that the Neurospora crassa genetic map was critical in narrowing the possible candidate mutations in a strain to a small number in a limited, defined region of the genome. Here in this study, we utilize a resequencing strategy to identify the mutations underlying the gluc-1 and gluc-2 genes in N. crassa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Theory of criticality for quantum ferroelectric metals

A variety of compounds, for example, doped paraelectrics and polar metals, exhibit both ferroelectricity and correlated electronic phenomena such as low-density superconductivity and anomalous transport. Characterizing such properties is tied to understanding the quantum dynamics of inversion symmetry breaking in the presence of itinerant electrons. Here, we present a comprehensive analysis of the properties of a metal near a quantum critical transition to a ferroelectric state, in both two and three dimensions. In this study, starting from a minimal model of electrons coupled to a transverse polar phonon via a Rashba-type spin-orbit interaction, we compute the dynamical response of both electrons and phonons. We find that the system can evince both Fermi and non-Fermi liquid phases, as well as enhanced pairing in both singlet and triplet channels. Furthermore, we systematically compute corrections to one-loop theory and find a tendency to quantum order-by-disorder, leading to a phase diagram that can include second-order, first-order, and finite-momentum phase transitions. Finally, we show that the entire phase diagram can be controlled via application of external strain, either compressive or volume-preserving. Our results provide a map of the dynamical and thermodynamical phase space of quantum ferroelectic metals, which can serve in characterizing existing materials and in seeking applications for quantum technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1984

Tectonic lineaments in the cenozoic volcanics of southern Guatemala: Evidence for a broad continental plate boundary zone

The northern Caribbean plate boundary has been undergoing left lateral strike slip motion since middle Tertiary time. The western part of the boundary occurs in a complex tectonic zone in the continental crust of Guatemala and southernmost Mexico, along the Chixoy-Polochic, Motogua and possibly Jocotan-Chamelecon faults. Prominent lineaments visible in radar imagery in the Neogene volcanic belt of southern Guatemala and western El Salvador were mapped and interpreted to suggest southwest extensions of this already broad plate boundary zone. Because these extensions can be traced beneath Quaternary volcanic cover, it is thought that this newly mapped fault zone is active and is accommodating some of the strain related to motion between the North American and Caribbean plates. Onshore exposures of the Motoqua-Polochic fault systems are characterized by abundant, tectonically emplaced ultramafic rocks. A similar mode of emplacement for these off shore ultramafics, is suggested.

Baltuck, M.↗
NASA NTRS2003

Tensor Fields for Use in Fractional-Order Viscoelasticity

To be able to construct viscoelastic material models from fractional0order differentegral equations that are applicable for 3D finite-strain analysis requires definitions for fractional derivatives and integrals for symmetric tensor fields, like stress and strain. We define these fields in the body manifold. We then map them ito spatial fields expressed in terms of an Eulerian or Lagrangian reference frame where most analysts prefer to solve boundary problems.

Freed, Alan D.↗
NASA NTRS2004

Malaria Modeling using Remote Sensing and GIS Technologies

Malaria has been with the human race since the ancient time. In spite of the advances of biomedical research and the completion of genomic mapping of Plasmodium falciparum, the exact mechanisms of how the various strains of parasites evade the human immune system and how they have adapted and become resistant to multiple drugs remain elusive. Perhaps because of these reasons, effective vaccines against malaria are still not available. Worldwide, approximately one to three millions deaths are attributed to malaria annually. With the increased availability of remotely sensed data, researchers in medical entomology, epidemiology and ecology have started to associate environmental and ecological variables with malaria transmission. In several studies, it has been shown that transmission correlates well with certain environmental and ecological parameters, and that remote sensing can be used to measure these determinants. In a NASA project, we have taken a holistic approach to examine how remote sensing and GIs can contribute to vector and malaria controls. To gain a better understanding of the interactions among the possible promoting factors, we have been developing a habitat model, a transmission model, and a risk prediction model, all using remote sensing data as input. Our objectives are: 1) To identify the potential breeding sites of major vector species and the locations for larvicide and insecticide applications in order to reduce costs, lessen the chance of developing pesticide resistance, and minimize the damage to the environment; 2) To develop a malaria transmission model characterizing the interactions among hosts, vectors, parasites, landcover and environment in order to identify the key factors that sustain or intensify malaria transmission, and 3) To develop a risk model to predict the occurrence of malaria and its transmission intensity using epidemiological data and satellite-derived or ground-measured environmental and meteorological data.

Kiang, Richard↗
NASA NTRS2003

Ventricular filling slows epicardial conduction and increases action potential duration in an optical mapping study of the isolated rabbit heart

INTRODUCTION: Mechanical stimulation can induce electrophysiologic changes in cardiac myocytes, but how mechanoelectric feedback in the intact heart affects action potential propagation remains unclear. METHODS AND RESULTS: Changes in action potential propagation and repolarization with increased left ventricular end-diastolic pressure from 0 to 30 mmHg were investigated using optical mapping in isolated perfused rabbit hearts. With respect to 0 mmHg, epicardial strain at 30 mmHg in the anterior left ventricle averaged 0.040 +/- 0.004 in the muscle fiber direction and 0.032 +/- 0.006 in the cross-fiber direction. An increase in ventricular loading increased average epicardial activation time by 25%+/- 3% (P < 0.0001) and correspondingly decreased average apparent surface conduction velocity by 16%+/- 7% (P = 0.007). Ventricular loading did not significantly alter action potential duration at 20% repolarization (APD20) but did at 80% repolarization (APD80), from 179 +/- 7 msec to 207 +/- 5 msec (P < 0.0001). The dispersion of APD20 was decreased with loading from 19 +/- 2 msec to 13 +/- 2 msec (P = 0.024), whereas the dispersion of APD80 was not significantly changed. These electrophysiologic changes with ventricular loading were not affected by the nonspecific stretch-activated channel blocker streptomycin (200 microM) and were not attributable to changes in myocardial perfusion or the presence of an electromechanical decoupling agent (butanedione monoxime) during optical mapping. CONCLUSION: Acute loading of the left ventricle of the isolated rabbit heart decreased apparent epicardial conduction velocity and increased action potential duration by a load-dependent mechanism that may not involve stretch-activated channels.

NASA Program Biomedical Research and Countermeasur↗
NASA NTRS2017

Curved Displacement Transfer Functions for Geometric Nonlinear Large Deformation Structure Shape Predictions

For shape predictions of structures under large geometrically nonlinear deformations, Curved Displacement Transfer Functions were formulated based on a curved displacement, traced by a material point from the undeformed position to deformed position. The embedded beam (depth-wise cross section of a structure along a surface strain-sensing line) was discretized into multiple small domains, with domain junctures matching the strain-sensing stations. Thus, the surface strain distribution could be described with a piecewise linear or a piecewise nonlinear function. The discretization approach enabled piecewise integrations of the embedded-beam curvature equations to yield the Curved Displacement Transfer Functions, expressed in terms of embedded beam geometrical parameters and surface strains. By entering the surface strain data into the Displacement Transfer Functions, deflections along each embedded beam can be calculated at multiple points for mapping the overall structural deformed shapes. Finite-element linear and nonlinear analyses of a tapered cantilever tubular beam were performed to generate linear and nonlinear surface strains and the associated deflections to be used for validation. The shape prediction accuracies were then determined by comparing the theoretical deflections with the finiteelement- generated deflections. The results show that the newly developed Curved Displacement Transfer Functions are very accurate for shape predictions of structures under large geometrically nonlinear deformations.

displacement theory↗
NASA NTRS1998

Determination of Yield and Flow Surfaces for Inconel 718 Under Axial-Torsional Loading at Temperatures Up to 649 C

An experimental program to determine flow surfaces has been established and implemented for solution annealed and aged IN718. The procedure involved subjecting tubular specimens to various ratios of axial-torsional stress at temperatures between 23 and 649 C and measuring strain with a biaxial extensometer. Each stress probe corresponds to a different direction in stress space, and unloading occurs when a 30 microstrain (1 micro eplison = 10(exp -6) mm/mm) offset is detected. This technique was used to map out yield loci in axial-torsional stress space. Flow surfaces were determined by post-processing the experimental data to determine the inelastic strain rate components. Surfaces of constant inelastic strain rate (SCISRS) and surfaces of constant inelastic power (SCIPS) were mapped out in the axial-shear stress plane. The von Mises yield criterion appeared to closely fit the initial loci for solutioned IN718 at 23 C. However, the initial loci for solutioned IN718 at 371 and 454 C, and all of the initial loci for aged IN718 were offset in the compression direction. Subsequent loci showed translation, distortion, and for the case of solutioned IN718, a slight cross effect. Aged IN718 showed significantly more hardening behavior than solutioned IN718.

Gil, Christopher M.↗