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At least 1,189 records · Page 66

Metagenomic clustering links specific metabolic functions to globally relevant ecosystems

ABSTRACT Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome’s functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute’s Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data. IMPORTANCE Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome’s metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.

54 ENVIRONMENTAL SCIENCES↗

Aspects of scaling and scalability for flow-based sampling of lattice QCD

Recent applications of machine-learned normalizing flows to sampling in lattice field theory suggest that such methods may be able to mitigate critical slowing down and topological freezing. However, these demonstrations have been at the scale of toy models, and it remains to be determined whether they can be applied to state-of-the-art lattice quantum chromodynamics calculations. Assessing the viability of sampling algorithms for lattice field theory at scale has traditionally been accomplished using simple cost scaling laws, but as we discuss in this work, their utility is limited for flow-based approaches. We conclude that flow-based approaches to sampling are better thought of as a broad family of algorithms with different scaling properties, and that scalability must be assessed experimentally.

Abbott, Ryan↗

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

59 BASIC BIOLOGICAL SCIENCES↗

Integration of pH Control into Chi.Bio Reactors and Demonstration with Small-Scale Enzymatic Poly(ethylene terephthalate) Hydrolysis

Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1–2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.

09 BIOMASS FUELS↗

In situ monitoring of microstructure evolution during thermal processing of uranium-zirconium alloys using laser-generated ultrasound

In this study, laser-generated ultrasound was used to monitor microstructure evolution during thermal processing of as-cast, polycrystalline binary uranium-zirconium metallic fuel alloys with compositions of U-20wt.%Zr (U-20Zr), U-50wt.%Zr (U-50Zr) and U-80wt.%Zr (U-80Zr). Ultrasonic waveforms were recorded during heating and cooling the samples from room temperature to >973 K and back. A phase transition temperature for all three compositions was estimated from the temperature at which an abrupt and rapid reduction in ultrasonic velocities was observed. Microstructural features on the length scale of tens of micrometers were inferred from the observation of scattering of ultrasonic waves by elastic heterogeneities above ~823 K in U-20Zr, while a hysteresis in the ultrasonic velocities of U-80Zr upon cooling was attributed to a partial retention of the high temperature phase following thermal annealing. The U-50Zr alloy exhibited a reversible viscoelastic response above 933 K, as evidenced by the observation of high frequency attenuation of the shear component of the waveforms at high temperature. Ultrasonic measurements were supplemented by in situ transmission electron microscopy (TEM). The TEM images revealed that the δ-U-Zr matrix in the three compositions underwent a spinodal decomposition above ~823 K into nanoscale regions. The ultrasonic measurements revealed larger, micron-scale structure evolution in the U-20Zr alloy at the same temperature. This large-scale structure is associated with heterogeneous regions having different Zr content. Our findings show the potential heating rate dependence of microstructural evolution in U-Zr alloys and highlight differences in the thermomechanical response and associated length scales during thermal annealing between single- and dual-phase compositions. These results demonstrate the utility of laser ultrasonics to rapidly and efficiently scan phase boundaries and monitor micrometer-scale structure evolution in metallic fuel alloys.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Gravitational field models for study of Earth mantle dynamics

The tectonic forces or stresses due to the small scale mantle flow under the South American plate are detected and determined by utilizing the harmonics of the geopotential field model. The high degree harmonics are assumed to describe the small scale mantle convection patterns. The input data used in the derivation of this model is made up of 840,000 optical, electronic, and laser observations and 1,656 5 deg x 5 deg mean free air anomalies. Although there remain some statistically questionable aspects of the high degree harmonics, it seems appropriate now to explore their implications for the tectonic forces or stress field under the crust.

Source record↗

MIRACL Co‐Simulation platform for control and operation of distributed wind in microgrid

Abstract This paper presents a co‐simulation platform (CSP) developed as a part of the “Microgrids, Infrastructure Resilience and Advanced Controls Launchpad (MIRACL)” project, hereafter called MIRACL‐CSP, to allow simulation‐based testing, demonstration, and evaluations of distributed wind under various grid operating conditions. MIRACL‐CSP provides modular interactions among the power distribution system, distributed wind, and utility decision‐making framework. A hierarchical engine for large‐scale infrastructure co‐simulations (HELICS) is used as the core engine of MIRACL‐CSP to establish time and information coordination among the MIRACL‐CSP modules. In this study, MIRACL‐CSP performance is demonstrated using the IEEE 123‐node test distribution grid modelled in GridLAB‐D and the utility decision support application modelled in Python. The functionality of MIRACL‐CSP is demonstrated through various grid operational scenarios in a microgrid and networked microgrid environment. A co‐simulation study is described that demonstrated MIRACL‐CSP capabilities for the microgrid operational scenario in the IEEE 123‐node test system. MIRACL‐CSP is a generic platform that facilitates distributed wind research for different test systems, applications, and valuation of distributed wind.

17 WIND ENERGY↗

Recent advances in combustion science related to hydrogen safety

Hydrogen is a key pillar in the global Net Zero strategy. Rapid scaling up of hydrogen production, transport, distribution and utilization is expected. This entails that hydrogen, which is traditionally an industrial gas, will come into proximity of populated urban areas and in some situations handled by the untrained public. To realize all their benefits, hydrogen and its technologies must be safely developed and deployed. The specific properties of hydrogen involving wide flammability range, low ignition energy and fast flame speed implies that any accidental release of hydrogen can be easily ignited. Comparing with conventional fuels, combustion systems fueled by hydrogen are also more prone to flame instability and abnormal combustion. This paper aims to provide a comprehensive review about combustion research related to hydrogen safety. It starts with a brief introduction which includes some overview about risk analysis, codes and standards. The core content covers ignition, fire, explosions and deflagration to detonation transition (DDT). Considering that DDT leads to detonation, and that detonation may also be induced directly under special circumstances, the subject of detonation is also included for completeness. The review covers laboratory, medium and large-scale experiments, as well as theoretical analysis and numerical simulation results. While highlights are provided at the end of each section, the paper closes with some concluding remarks highlighting the achievements and key knowledge gaps.

08 HYDROGEN↗

Impact of large-scale effects on mass transfer and concentration polarization in Reverse Osmosis membrane systems

Here, we present well-resolved computational fluid dynamics simulations of a large-scale reverse osmosis membrane-spacer configuration (1 m). Our computational model solves the flow and transport equations with variable solute-dependent properties. We utilize a high resolution computational mesh to resolve all relevant length scales associated with spacer-induced mixing and thin concentration boundary layers. An important contribution of this work is the development of a modified mass-transfer correlation that accounts for the development of the concentration boundary layer along the channel. A set of 2D axisymmetric simulations were performed for a spiral wound module layer with varying cross-flow conditions and spacer diameters which indicate a significant entrance length effect for concentration profile development at lower flow rates while mixing effects dominate at higher flow rates. The mass-transfer correlations at higher flow rates compare well with published correlations while a surrogate model for Sherwood number was obtained that depends on an additional similarity variable that accounted for entrance length effects at lower flow rates. Finally, a large-scale membrane-spacer design relevant to high-pressure reverse osmosis is studied with a non-uniform arrangement of spacers, which indicate a substantial saving in pressure drop (~40%) compared to traditional uniformly spaced pattern with minor variations (~2%) in concentration polarization, product water quality (~1%) and water recovery (~7%) compared to a uniform spacer pattern.

97 MATHEMATICS AND COMPUTING↗

Survey and Gap Prioritization of U.S. Electric Vehicle Charge Management Deployments

The goal of this study was to survey and characterize the scope of current technical and programmatic knowledge pertaining to EV charge management technologies and practices in the US and relevant international jurisdictions. This characterization of existing field demonstrations and knowledge derived were used to determine gaps in the SCM demonstration landscape. Addressing these gaps through research and demonstration could increase confidence in the U.S. that load management and EV charge control could achieve overarching societal benefits. A survey of charge management deployments and input from stakeholders was completed to determine the state-of-the-art of smart charge management (SCM) where SCM is defined as controlling the amount of power exchanged between chargers and EVs to meet customers' charging needs while also responding to external power demand or pricing signals to provide load management, resilience, or other benefits to the customer and electric grid. The survey was the basis of the gap analysis in this report and determines which areas are well understood, with high confidence, and which areas need further investigation. Existing examples of EV charge management are characterized here to determine aspects that are ready for widespread deployment and have been demonstrated in the field. These include demonstration studies, pilots, programs, and EV-specific tariffs. In all, 110 examples of charge management were characterized. The data sources were public literature and utility filings as well as targeted interviews. In addition, 43 interviews with stakeholders were conducted with a consistent set of questions used in each interview. This study prioritized gaps in demonstrated SCM capabilities based on 1) Urgency of the particular use-case to offset traditional grid assets, 2) Impact, extensibility, and scaling of results across the entire spectrum of 3000+ utility service territories including projected technical and market potential for a given grid service, and 3) Value of federal funding in addressing the gap, including potential to leverage and/or add scope to existing field demonstrations funded by other non-federal funding mechanisms.

33 ADVANCED PROPULSION SYSTEMS↗

Bridging particle and reactor scales in the simulation of biomass fast pyrolysis by coupling particle resolved simulation and coarse grained CFD-DEM

Efficient utilization of biomass is challenging due to the complexity of the feedstock at molecular, particle, and reactor scales. Direct coupling of particle scale model and reactor scale simulation is computationally infeasible. In this work, the results from a particle resolved simulation were used to calibrate the heat transfer and reaction kinetics of particles. A hybrid drag model was used to consider the different fluidization properties of sands and biomass particles. The computation cost was reduced using a coarse-grained Discrete Element Method (DEM). The simulated conversion rate, char yield, tar yield, and pyrolysis gas yield compare well with experiment. The residence time and axial distributions of biomass were also analyzed. This novel multi-scale method provides an efficient and accurate tool for the modeling of biomass pyrolysis reactors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Workflow to Rapidly Interrogate Multiscale Model Simulation Results Across Multiple Length Scales

Many tools can be used to visualize field and state variables for a single scale analysis so that the influence of relevant mechanisms can be evaluated. Finite element software is often utilized to simulate a unit cell of a material and visualize results at that scale. Material properties can be homogenized from individual constituents and local deformation, damage, and failure mechanisms can be evaluated within the unit cell due to globally applied boundary conditions. Such solutions can produce satisfactory results if a user is only interested in analyzing a single scale. But materials in general contain features across multiple length scales, and assumptions must be made when attempting to account for lower length scale phenomena within a higher length scale model. Multiscale modeling is an attractive means to model materials because detailed material responses can be tracked across multiple disparate length scales while reducing the amount of required assumptions. However, as the complexity of these models increases, a large amount of data can be produced, and data traceability can become increasingly more difficult. Field and state variables, which are naturally dependent on spatial position, may themselves be calculated from one or more lower length scale unit cell models each with their own appropriate field and state variables. The NASA Multiscale Analysis Tool (NASMAT) is one software that can be used to perform a multiscale analysis efficiently and output requested data at all length scales in the analysis. A companion open-source Python software, NASMAT PrePost, can be used to visualize NASMAT model results and rapidly interrogate multiscale data across multiple length scales. This presentation will demonstrate some of the key features of NASMAT PrePost on two multiscale problems by quickly displaying and demonstrating connectivity among multiscale results from large datasets.

Python↗

Thermal energy storage in concrete utilizing a thermosiphon heat exchanger

The performance of a lab-scale concrete thermal energy storage (TES) module with a 2-kWh thermal capacity is evaluated at temperatures up to 400 °C. The TES module uses conventional normal weight concrete with thermal and mechanical properties that are tailored for use as a solid thermal energy storage media. A thermosiphon heat exchanger is used to provide rapid heat transfer into the concrete module, which is reinforced with a steel pipe outer shell. The charging and discharging cycles are examined to assess the thermal performance of the concrete and thermosiphon. Based on the results of testing, the thermosiphon is able to repeatably charge the concrete module from 300 to 400 °C over a 4-h period. After 2250 total hours of charge and discharge cycles, there was no observed delamination between the concrete and the thermosiphon or the steel jacket reinforcement. Non-destructive measurements of the concrete indicated no significant degradation of the solid storage media. The experimental results are then used to validate a numerical model of the concrete TES module for parametric study. Finally, varying insulation conditions were analyzed using this model to determine practical configurations for regular operation of the proposed concrete TES module.

25 ENERGY STORAGE↗

Evaluating the Performance of Single and Double Moment Microphysics Schemes During a Synoptic-Scale Snowfall Event

Increases in computing resources have allowed for the utilization of high-resolution weather forecast models capable of resolving cloud microphysical and precipitation processes among varying numbers of hydrometeor categories. Several microphysics schemes are currently available within the Weather Research and Forecasting (WRF) model, ranging from single-moment predictions of precipitation content to double-moment predictions that include a prediction of particle number concentrations. Each scheme incorporates several assumptions related to the size distribution, shape, and fall speed relationships of ice crystals in order to simulate cold-cloud processes and resulting precipitation. Field campaign data offer a means of evaluating the assumptions present within each scheme. The Canadian CloudSat/CALIPSO Validation Project (C3VP) represented collaboration among the CloudSat, CALIPSO, and NASA Global Precipitation Measurement mission communities, to observe cold season precipitation processes relevant to forecast model evaluation and the eventual development of satellite retrievals of cloud properties and precipitation rates. During the C3VP campaign, widespread snowfall occurred on 22 January 2007, sampled by aircraft and surface instrumentation that provided particle size distributions, ice water content, and fall speed estimations along with traditional surface measurements of temperature and precipitation. In this study, four single-moment and two double-moment microphysics schemes were utilized to generate hypothetical WRF forecasts of the event, with C3VP data used in evaluation of their varying assumptions. Schemes that incorporate flexibility in size distribution parameters and density assumptions are shown to be preferable to fixed constants, and that a double-moment representation of the snow category may be beneficial when representing the effects of aggregation. These results may guide forecast centers in optimal configurations of their forecast models for winter weather and identify best practices present within these various schemes.

Molthan, Andrew L.↗

Venus Quadrangle Geological Mapping: Use of Geoscience Data Visualization Systems in Mapping and Training

We are currently investigating new technological developments in computer visualization and analysis in order to assess their importance and utility in planetary geological analysis and mapping [1,2]. Last year we reported on the range of technologies available and on our application of these to various problems in planetary mapping [3]. In this contribution we focus on the application of these techniques and tools to Venus geological mapping at the 1:5M quadrangle scale. In our current Venus mapping projects we have utilized and tested the various platforms to understand their capabilities and assess their usefulness in defining units, establishing stratigraphic relationships, mapping structures, reaching consensus on interpretations and producing map products. We are specifically assessing how computer visualization display qualities (e.g., level of immersion, stereoscopic vs. monoscopic viewing, field of view, large vs. small display size, etc.) influence performance on scientific analysis and geological mapping. We have been exploring four different environments: 1) conventional desktops (DT), 2) semi-immersive Fishtank VR (FT) (i.e., a conventional desktop with head-tracked stereo and 6DOF input), 3) tiled wall displays (TW), and 4) fully immersive virtual reality (IVR) (e.g., "Cave Automatic Virtual Environment," or Cave system). Formal studies demonstrate that fully immersive Cave environments are superior to desktop systems for many tasks [e.g., 4].

Head, James W.↗

ARIES/Flatirons Facility - Hydrogen System Capability Buildout

Under the Advanced Research for Integrated Energy Systems (ARIES) initiative, NREL will build out hydrogen system capabilities at the Flatirons campus. The hydrogen infrastructure at the Flatirons campus will include a research-ready megawatt-scale electrolyzer with hydrogen compression and storage, and a fuel cell system. This hardware will support H2@Scale goals by enabling integrated systems R&D (e.g., to demonstrate grid services, energy storage, renewable hydrogen production, and innovative end-use applications). The system will be coupled with the controllable grid interface at the Flatirons campus and will be designed with flexibility to provide a testbed for integrated electrolyzer R&D, hydrogen utilization R&D, and to study the science of scaling for hydrogen energy systems.

39 EE - Hydrogen and Fuel Cell Technologies (EE-3F↗

Tortuosity measurement and the effects of finite pulse widths on xenon gas diffusion NMR studies of porous media

We have extended the utility of NMR as a technique to probe porous media structure over length scales of approximately 100-2000 microm by using the spin 1/2 noble gas 129Xe imbibed into the system's pore space. Such length scales are much greater than can be probed with NMR diffusion studies of water-saturated porous media. We utilized Pulsed Gradient Spin Echo NMR measurements of the time-dependent diffusion coefficient, D(t), of the xenon gas filling the pore space to study further the measurements of both the pore surface-area-to-volume ratio, S/V(p), and the tortuosity (pore connectivity) of the medium. In uniform-size glass bead packs, we observed D(t) decreasing with increasing t, reaching an observed asymptote of approximately 0.62-0.65D(0), that could be measured over diffusion distances extending over multiple bead diameters. Measurements of D(t)/D(0) at differing gas pressures showed this tortuosity limit was not affected by changing the characteristic diffusion length of the spins during the diffusion encoding gradient pulse. This was not the case at the short time limit, where D(t)/D(0) was noticeably affected by the gas pressure in the sample. Increasing the gas pressure, and hence reducing D(0) and the diffusion during the gradient pulse served to reduce the previously observed deviation of D(t)/D(0) from the S/V(p) relation. The Pade approximation is used to interpolate between the long and short time limits in D(t). While the short time D(t) points lay above the interpolation line in the case of small beads, due to diffusion during the gradient pulse on the order of the pore size, it was also noted that the experimental D(t) data fell below the Pade line in the case of large beads, most likely due to finite size effects.

Non-NASA Center↗