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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Impact of Lateral Groundwater Flow and Subsurface Lower Boundary Conditions on Atmospheric Boundary Layer Development over Complex Terrain

Credible soil moisture redistribution schemes are essential to meteorological models, as lower boundary moisture influences the balance of surface turbulent fluxes and atmospheric boundary layer (ABL) development. While land surface models (LSMs) have vastly improved in their hydrologic representation, several commonly held assumptions, such as free-draining lower boundary, one-dimensional moisture flux, and lack of groundwater representation, can bias the terrestrial water balance. This study explores the impact of LSM hydrology representation on ABL development in the Weather Research and Forecasting (WRF) meteorological model. The results of summertime WRF simulations with Noah LSM, characterized by 2-m-thick soil and one-dimensional flow, are shown for a domain in the Colorado Rocky Mountain headwaters region. A reference WRF simulation is compared to 1) the same model with soil moisture initialized by the hydrologic model ParFlow; 2) a deep, free-draining simulation; and 3) WRF coupled to ParFlow, a three-dimensional, integrated groundwater-surface water model. Results show that both lateral transport of groundwater and the rate of drainage from the lower soil layer can weaken or reverse the coupling strength between evaporative fraction and ABL over a 5-month summer period. The resulting shifts in low-level moist convection in river valleys and thermally driven airflows yield strengthened anabatic upslope winds and perturbations to regional precipitation.

Forrester, Mary M.↗
DOE OSTI2017

Laterally coupled distributed feedback type-I quantum well cascade diode lasers emitting near 3.22 μm

The laterally coupled distributed feedback (LC-DFB) GaSb-based type-I quantum well cascade diode lasers using the second- and the sixth-order gratings to stabilize the output spectrum near 3.22 μm were designed and fabricated in this paper. The laser heterostructure contained three cascades. The devices were manufactured using a single dry etching step defining the ~5-μm-wide ridge with ~5-μm-wide gratings sections adjacent to the ridge sides. The grating coupling coefficients were estimated to be about 1 cm -1 . The stability of the single-frequency operation was ensured by alignment of the DFB mode to the relatively wide gain peak. The 2-mm-long second-order LC-DFB lasers generated above 10 mW of continuous-wave (CW) output power at 20°C in epi-side-up configuration and demonstrated power conversion efficiency above 2%. The sixth-order LC-DFB lasers showed lower efficiency but still generated several milliwatts of CW output power. Finally, the devices demonstrated a CW current tuning range of about 3.5 nm at the temperature of 20°C.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma . A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Diamond heteroepitaxial lateral overgrowth

A method of diamond heteroepitaxial lateral overgrowth is demonstrated which utilizes a photolithographic metal mask to pattern a thin (001) epitaxial diamond surface. Significant structural improvement was found, with a threading dislocation density reduced by two orders of magnitude at the top surface of a thick overgrown diamond layer. In the initial stage of overgrowth, a reduction of diamond Raman linewidth in the overgrown area was also realized. Thermally-induced stress and internal stress were determined by Raman spectroscopy of adhering and delaminated diamond films. As a result, the internal stress is found to decrease as sample thickness increases.

36 MATERIALS SCIENCE↗
DOE OSTI2013

New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes

Algorithmic methods for gene prediction have been developed and successfully applied to many different prokaryotic genome sequences. As the set of genes in a particular genome is not homogeneous with respect to DNA sequence composition features, the GeneMark.hmm program utilizes two Markov models representing distinct classes of protein coding genes denoted "typical" and "atypical". Atypical genes are those whose DNA features deviate significantly from those classified as typical and they represent approximately 10% of any given genome. In addition to the inherent interest of more accurately predicting genes, the atypical status of these genes may also reflect their separate evolutionary ancestry from other genes in that genome. We hypothesize that atypical genes are largely comprised of those genes that have been relatively recently acquired through lateral gene transfer (LGT). If so, what fraction of atypical genes are such bona fide LGTs? We have made atypical gene predictions for all fully completed prokaryotic genomes; we have been able to compare these results to other "surrogate" methods of LGT prediction.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Chlamydia psittaci Infection

Chlamydia psittaci is the causative agent of psittacosis, a worldwide zoonotic disease. A rapid, specific, and sensitive diagnostic assay would be benefit for C. psittaci infection control. In this study, an assay combining recombinase-aided amplification and a lateral flow strip (RAA-LF) for the detection of active C. psittaci infection was developed. The RAA-LF assay targeted the CPSIT_RS02830 gene of C. psittaci and could be accomplished in 15 min at a single temperature (39°C). The analytical sensitivity of the assay was as low as 1 × 10 0 copies/μl and no cross-reaction with some other intracellular pathogens was observed. Moreover, all feces samples from mice infected with C. psittaci at day-1 post-infection were positive in the RAA-LF assay. In conclusion, the RAA-LF assay provides a convenient, rapid, specific and sensitive method for detection of active C. psittaci infection and it is also suitable for C. psittaci detection in field.

Jiao, Jun↗
DOE OSTI2025

Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer’s Disease, Parkinson’s Disease, and Amyotrophic Lateral Sclerosis

Background: Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. Methods: Using untargeted mass spectrometry-based metabolomics and 16S sequencing of human stool, we investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs—amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson’s disease (PD)—and healthy controls (HC). Results: We discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and gut dysbiosis in NDDs. DHPS was downregulated in AD, ALS, and PD, while bacteria involved in DHPS metabolism, Eubacterium and Desulfovibrio, were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS, suggesting a potential role in DHPS metabolism. A catabolic product of DHPS is hydrogen sulfide, and when in excess, it is known to promote inflammation, oxidative stress, mitochondrial damage, and gut dysbiosis, known hallmarks of NDDs. Conclusions: These findings suggest that cryptic sulfur metabolism via DHPS is a potential missing link in our current understanding of gut dysbiosis associated with NDD onset and progression. As this was a hypothesis generating study, more work is needed to elucidate the role of DHPS in gut dysbiosis and neurodegenerative diseases.

Nutrition & Dietetics↗
DOE OSTI2024

Over 600 V Lateral AlN-on-AlN Schottky Barrier Diodes with Ultra-Low Ideality Factor

Abstract This letter reports the demonstration of lateral AlN Schottky barrier diodes (SBDs) on single-crystal AlN substrates by metalorganic CVD (MOCVD) with an ultra-low ideality factor ( η ) of 1.65, a high Schottky barrier height of 1.94 eV, a breakdown voltage ( BV ) of 640 V, and a record high normalized BV by the anode-to-cathode distance. The device current was dominated by thermionic emission, while most previously reported AlN SBDs suffered from defect-induced current with higher η (>4). This work represents a significant step towards high-performance ultra-wide bandgap AlN-based high-voltage and high-power devices.

Physics↗
DOE OSTI2020

Dynamics of Laterally Propagating Flames in X-Ray Bursts. I. Burning Front Structure

We investigate the structure of laterally propagating flames through the highly stratified burning layer in an X-ray burst. Two-dimensional hydrodynamics simulations of flame propagation are performed through a rotating plane-parallel atmosphere, exploring the structure of the flame. We discuss the approximations needed to capture the length and timescales at play in an X-ray burst and describe the flame acceleration observed. Finally, our studies complement other multidimensional studies of burning in X-ray bursts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Dynamics of Laterally Propagating Flames in X-Ray Bursts. II. Realistic Burning and Rotation

In this work, we continue to investigate two-dimensional laterally propagating flames in type I X-ray bursts using fully compressible hydrodynamics simulations. In the current study we relax previous approximations where we artificially boosted the flames. We now use more physically realistic reaction rates, thermal conductivities, and rotation rates, exploring the effects of neutron star rotation rate and thermal structure on the flame. We find that at lower rotation rates the flame becomes harder to ignite, whereas at higher rotation rates the nuclear burning is enhanced by increased confinement from the Coriolis force and the flame propagates steadily. At higher crustal temperatures, the flame moves more quickly and accelerates as it propagates through the atmosphere. If the temperature is too high, instead of a flame propagating across the surface the entire atmosphere burns uniformly. Our findings could have implications for the relationship between observed burst rise times and neutron star rotation and accretion rates. All of the software used for these simulations is freely available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A distributed temperature profiling system for vertically and laterally dense acquisition of soil and snow temperature

Abstract. Measuring soil and snow temperature with high vertical and lateral resolution is critical for advancing the predictive understanding of thermal and hydro-biogeochemical processes that govern the behavior of environmental systems. Vertically resolved soil temperature measurements enable the estimation of soil thermal regimes, frozen-/thawed-layer thickness, thermal parameters, and heat and/or water fluxes. Similarly, they can be used to capture the snow depth and the snowpack thermal parameters and fluxes. However, these measurements are challenging to acquire using conventional approaches due to their total cost, their limited vertical resolution, and their large installation footprint. This study presents the development and validation of a novel distributed temperature profiling (DTP) system that addresses these challenges. The system leverages digital temperature sensors to provide unprecedented, finely resolved depth profiles of temperature measurements with flexibility in system geometry and vertical resolution. The integrated miniaturized logger enables automated data acquisition, management, and wireless transfer. A novel calibration approach adapted to the DTP system confirms the factory-assured sensor accuracy of ±0.1 ∘C and enables improving it to ±0.015 ∘C. Numerical experiments indicate that, under normal environmental conditions, an additional error of 0.01 % in amplitude and 70 s time delay in amplitude for a diurnal period can be expected, owing to the DTP housing. We demonstrate the DTP systems capability at two field sites, one focused on understanding how snow dynamics influence mountainous water resources and the other focused on understanding how soil properties influence carbon cycling. Results indicate that the DTP system reliably captures the dynamics in snow depth and soil freezing and thawing depth, enabling advances in understanding the intensity and timing in surface processes and their impact on subsurface thermohydrological regimes. Overall, the DTP system fulfills the needs for data accuracy, minimal power consumption, and low total cost, enabling advances in the multiscale understanding of various cryospheric and hydro-biogeochemical processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The Importance of Freeze/Thaw Cycles on Lateral Transport in Ice-Wedge Polygons: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "The importance of freeze/thaw cycles on lateral transport in ice-wedge polygons". The dataset includes xml input/configuration files. These files are compatible with the ATS version 1.0 and higher. The mesh folder contains mesh files used for high-centered polygon (hcp) and low-centered polygon (lcp). The mesh files represent the transect of the polygonal tundra (Fig 1). Here we used two types of mesh with impermeable layer and without. The mesh with an impermeable layer corresponds to the synthetic permafrost (no freezeup case). The freeze up case uses mesh without impermeable layer to simulated frozen ground start at the same depth where the impermeable layer is for the no freezeup case. The meteorological data used drive the model saved in the "inputs" folder. The processed tracer flow rates are saved in the "tracer-flow-ratesCfolder. To plot figures 1 and 2, we used VisIt software. To plot all the flow rates, we used ipython notebook script. All required inputs are saved in "freezeup" and "no freezeup" folders. Each folder includes the corresponding "lcp" and "hcp" folders. The "freezeup" folder has also flat-centered polygon (fcp) case, low porosity "lpor", and low permeability "lper" cases. Included are *.xml, *.exo, *.h5, *pdf, *.ipynb, *.sh, *.py, and *.out files. NGEE Arctic Project Summary: The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A Distributed Temperature Profiling System for Vertically and Laterally Dense Acquisition of Soil and Snow Temperature: Supporting Data

This dataset was used to assess the potential of a Distributed Temperature Profiling System developed and presented in the article named "A Distributed Temperature Profiling System for Vertically and Laterally Dense Acquisition of Soil and Snow Temperature" and submitted to Cryosphere. There are three comma-delimited data files (.csv). Each of them contains snow or soil temperature with times (UTC) in the first column and temperature at various vertical distance from the ground surface (positive means in air/snow) or below the ground surface (negative means in soil). The measurements were acquired every 15 minutes. Data collected at the East River, Colorado site with two probes: 1) measuring air/snow temperature from 1.1 m above the ground surface to the ground surface (with 5 or 10 cm spacing between sensors) and 2) measuring soil temperature from the ground surface to 0.7 m depth (with 5 or 10 cm spacing between sensors). Data collected at the Teller road (mile 27) site near Nome, Alaska with one probe: measuring soil temperature from 5 cm above the ground surface to 1.05 m depth (with 5 or 10 cm spacing between sensors). Additional metadata included in *.csv and *.pdf files. NGEE Arctic Project Summary: The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗