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At least 1,567 records · Page 87

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Abstract Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

59 BASIC BIOLOGICAL SCIENCES↗

Hierarchical transfer learning: an agile and equitable strategy for machine-learning interatomic models

Machine-learned interatomic models are growing in popularity due to their ability to afford near quantum-accurate predictions for complex phenomena with orders-of-magnitude greater computational efficiency. However, these models struggle when applied to systems of many element types due to the approximately exponential increase in number of parameters that must be determined. To mitigate this challenge, we present a new hierarchical transfer learning approach that allows the fitting problem to be decomposed into smaller independent and reusable parameter blocks that enable development of explicitly chemically extensible ML-IAM. Application of this strategy is demonstrated for C and N mixtures under conditions ranging from nominally ambient to ~10,000 K and 200 GPa for compositions from 0 to 100% N. Ultimately, this strategy makes model generation for chemically complex systems more tractable and efficient, facilitates comprehensive model validation, and makes ML-IAM development for problems of this nature more accessible to users with limited access to extreme computing infrastructure.

Lindsey, Rebecca K. [Univ. of Michigan, Ann Arbor,↗

Electromagnetic levitation containerless processing of metallic materials in microgravity: rapid solidification

Space levitation processing allows researchers to conduct benchmark tests in an effort to understand the physical phenomena involved in rapid solidification processing, including alloy thermodynamics, nucleation and growth, heat and mass transfer, solid/liquid interface dynamics, macro- and microstructural evolution, and defect formation. Supported by ground-based investigations, a major thrust is to develop and refine robust computational tools based on theoretical and applied approaches. This work is accomplished in conjunction with experiments designed for precise model validation with application to a broad range of industrial processes.

42 ENGINEERING↗

Six years of ecosystem-atmosphere greenhouse gas fluxes measured in a sub-boreal forest

Carbon dioxide (CO 2 ), methane (CH 4 ), and nitrous oxide (N 2 O) are the greenhouse gases largely responsible for anthropogenic climate change. Natural plant and microbial metabolic processes play a major role in the global atmospheric budget of each. We have been studying ecosystem-atmosphere trace gas exchange at a sub-boreal forest in the northeastern United States for over two decades. Historically our emphasis was on turbulent fluxes of CO 2 and water vapor. In 2012 we embarked on an expanded campaign to also measure CH 4 and N 2 O. Here we present continuous tower-based measurements of the ecosystem-atmosphere exchange of CO 2 and CH 4 , recorded over the period 2012–2018 and reported at a 30-minute time step. Additionally, we describe a five-year (2012–2016) dataset of chamber-based measurements of soil fluxes of CO 2 , CH 4 , and N 2 O (2013–2016 only), conducted each year from May to November. These data can be used for process studies, for biogeochemical and land surface model validation and benchmarking, and for regional-to-global upscaling and budgeting analyses.

54 ENVIRONMENTAL SCIENCES↗

A Dataset of 3D Structural and Simulated Transport Properties of Complex Porous Media

Physical processes that occur within porous materials have wide-ranging applications including - but not limited to - carbon sequestration, battery technology, membranes, oil and gas, geothermal energy, nuclear waste disposal, water resource management. The equations that describe these physical processes have been studied extensively; however, approximating them numerically requires immense computational resources due to the complex behavior that arises from the geometrically-intricate solid boundary conditions in porous materials. Here, we introduce a new dataset of unprecedented scale and breadth, DRP-372: a catalog of 3D geometries, simulation results, and structural properties of samples hosted on the Digital Rocks Portal. The dataset includes 1736 flow and electrical simulation results on 217 samples, which required more than 500 core years of computation. This data can be used for many purposes, such as constructing empirical models, validating new simulation codes, and developing machine learning algorithms that closely match the extensive purely-physical simulation. This article offers a detailed description of the contents of the dataset including the data collection, simulation schemes, and data validation.

3D images↗

In situ melt pool measurements for laser powder bed fusion using multi sensing and correlation analysis

Laser powder bed fusion is a promising technology for local deposition and microstructure control, but it suffers from defects such as delamination and porosity due to the lack of understanding of melt pool dynamics. To study the fundamental behavior of the melt pool, both geometric and thermal sensing with high spatial and temporal resolutions are necessary. This work applies and integrates three advanced sensing technologies: synchrotron X-ray imaging, high-speed IR camera, and high-spatial-resolution IR camera to characterize the evolution of the melt pool shape, keyhole, vapor plume, and thermal evolution in Ti–6Al–4V and 410 stainless steel spot melt cases. Aside from presenting the sensing capability, this paper develops an effective algorithm for high-speed X-ray imaging data to identify melt pool geometries accurately. Preprocessing methods are also implemented for the IR data to estimate the emissivity value and extrapolate the saturated pixels. Quantifications on boundary velocities, melt pool dimensions, thermal gradients, and cooling rates are performed, enabling future comprehensive melt pool dynamics and microstructure analysis. The study discovers a strong correlation between the thermal and X-ray data, demonstrating the feasibility of using relatively cheap IR cameras to predict features that currently can only be captured using costly synchrotron X-ray imaging. Such correlation can be used for future thermal-based melt pool control and model validation.

47 OTHER INSTRUMENTATION↗

Quantifying motion blur by imaging shock front propagation with broadband and narrowband X-ray sources

Time-integrated radiography using MeV Bremsstrahlung X-ray sources is the norm for imaging during system-level testing of components and structures under dynamic condition. One source of error in the analysis of the time-integrated radiography data sets stems from motion blur which smears out sharp interfaces to a greater degree with longer exposure times, which become necessary to provide sufficient signal-to-noise with low X-ray penetration of objects of interest. To quantify motion blur, a 1D shock wave through PMMA was investigated experimentally at The Dynamic Compression Sector at The Advanced Photon Source (DCS@APS) with tapered broadband and 25.46 ± 1.06 keV narrowband X-rays. Four cameras with different exposure times were used for each experiment to compare the effect that exposure time has on motion blur. In addition, our methodology to accurately simulate motion blur in terms of transmission and shape is presented and compared to our experimental results and quantified. There is a high level of agreement between the experimental and simulation results across the range of data sets investigated in this study with a percent difference range of 0.29–1.31% for the four shots. The methodology of this work serves as a steppingstone towards a physically validated model that could be used in conjunction with experimental results to deconvolve physical parameters, densities, and interfaces of interest in a way that would not be possible with experimental results alone.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A multi-ancestry GWAS of Fuchs corneal dystrophy highlights the contributions of laminins, collagen, and endothelial cell regulation

Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular etiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program followed by multi-ancestry meta-analysis with the previous largest FECD GWAS, for a total of 3970 cases and 333,794 controls. We confirm the previous four loci, and identify eight novel loci: SSBP3, THSD7A, LAMB1, PIDD1, RORA, HS3ST3B1, LAMA5, and COL18A1. We further confirm the TCF4 locus in GWAS for admixed African and Hispanic/Latino ancestries and show an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling, validated through homology, suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and colocalization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.

59 BASIC BIOLOGICAL SCIENCES↗

Slippery liquid infused porous surface (SLIPS) condensers for high efficiency air gap membrane distillation

Abstract To address growing water scarcity, we must improve the energy efficiency of thermal desalination technologies such as air gap membrane distillation. However, promising functional materials such as slippery liquid infused porous surfaces have not yet implemented for any desalination technology. Here, we fabricate and test slippery liquid infused porous surfaces (using Krytox 16,256 lubricant and CuO nanostructures) in an air gap membrane distillation apparatus. System-level transport models, validated by experimental data, establish a framework for improving performance through enhanced condensation surfaces. Results are obtained across a range of temperatures (50–80 °C), salinities (5–105 g/kg), and module lengths. We find that small air gap thickness and efficient droplet shedding significantly improves performance. The CuO Krytox process achieves these with a conductive-self-limiting coating, high nanostructure rugosity, strong covalent and metallic bonding, high hydrophobicity, minimal droplet pinning sites, and ultra-low contact angle hysteresis. The greatest efficiency enhancement from SLIPS is derived from the improved droplet shedding, which allows for reduced gap sizes without flooding, and is further augmented by the increased permeate flux.

Yogi, Yashwant S.↗

The Role of Climate Covariability on Crop Yields in the Conterminous United States

The covariability of temperature (T), precipitation (P) and radiation (R) is an important aspect in understanding the climate influence on crop yields. Here in this paper, we analyze county-level corn and soybean yields and observed climate for the period 1983–2012 to understand how growing-season (June, July and August) mean T, P and R influence crop yields jointly and in isolation across the CONterminous United States (CONUS). Results show that nationally averaged corn and soybean yields exhibit large interannual variability of 21% and 22%, of which 35% and 32% can be significantly explained by T and P, respectively. By including R, an additional of 5% in variability can be explained for both crops. Using partial regression analyses, we find that studies that ignore the covariability among T, P, and R can substantially overestimate the sensitivity of crop yields to a single climate factor at the county scale. Further analyses indicate large spatial variation in the relative contributions of different climate variables to the variability of historical corn and soybean yields. Finally, the structure of the dominant climate factors did not change substantially over 1983–2012, confirming the robustness of the findings, which have important implications for crop yield prediction and crop model validations.

54 ENVIRONMENTAL SCIENCES↗

Resolving Local Configurational Contributions to X-ray and Neutron Radial Distribution Functions Within Solutions of Concentrated Electrolytes – A Case Study of Concentrated NaOH

Extreme conditions of complex materials often lead to a manifold of local environments that challenge characterization and require new advances at the intersection of modern experimental and theoretical techniques. In this contribution, highly caustic and viscous aqueous NaOD solutions were characterized with a combination of X-ray and neutron radial distribution function (RDF) analyses, molecular dynamics simulations and sub-ensemble analysis. The interpretation of the experimental RDFs extends beyond the traditional understanding of atom-pair interactions and to the individual contributions of specific molecular-scale configurations (below 3.5 Å). This integrated approach yields unique insight into the complex and significant breath of ion solvation and pairing structural motifs present, the experimental sensitivity of RDFs to changes in local geometries, and the challenge of experimentally differentiating the ensemble of all superimposed local environments — a feature of increasing importance within the extreme condition of high ionic strength. This study was facilitated by the development of a chemically resistant sample cell for in-situ neutron total scattering measurements of highly caustic materials at elevated temperature and pressure conditions. Advancing these integrated capabilities is critical for ongoing model validation efforts and for extending the predictive capabilities needed for the extremes of chemical composition, aiding a variety of industrial processes that include advanced nuclear waste remediation and metal refining strategies.

Semrouni, David↗

Destructive reverse bias pinning in perovskite/silicon tandem solar modules caused by perovskite hysteresis under dynamic shading

In this work, we demonstrate how perovskite hysteresis can result in permanent reductions in power output in perovskite/silicon tandem modules—including irreversible hotspot-induced damage—from only brief periods of shading. We show that reverse bias events in which a perovskite cell is biased above a threshold voltage—which in this work we find to be as low as –1.1 V—produces a temporary reduction in power output that is of sufficient magnitude to keep the cell pinned in reverse bias after the shading event ends. As a hysteretic phenomena, this crucial failure mode may be overlooked by static models of perovskite-based solar cells. Higher reverse bias voltages exacerbate the temporary reduction in short-circuit photocurrent, which is also sensitive to the level of illumination under reverse bias. Numerical device modelling demonstrates that this effect is consistent with our understanding of perovskite hysteresis as a consequence of mobile ion-electron coupling controlling rates of non-radiative recombination over time. Measurements of the dynamic response of single-junction perovskite cells are extrapolated to two-terminal and four-terminal perovskite/silicon tandem module modelling. We validate these models with measurements from an equivalent electronic circuit that represents a two-terminal perovskite–silicon tandem mini module. Two module-level solutions are discussed that address this issue, which includes increasing the number of bypass diodes and choosing better suited silicon bottom cells with higher shunter resistance in two-terminal tandem modules.

14 SOLAR ENERGY↗

In-situ Experiments to Capture the Evolution of Microstructure During Phase Transformation of Titanium Under Dynamic Loading

Under sufficient stresses, such as during dynamic loading, titanium experiences a phase transformation from hcp alpha phase to hexagonal omega phase. Omega phase is often retained in the microstructure after unloading, and has a strong influence on subsequent mechanical properties. Simulations suggest there are multiple pathways and underlying mechanisms for this transformation. Due to the incredibly short timescales involved, experimental measurements for model validation have been difficult. However, new capabilities at the Advanced Photon Source have enabled diffraction measurements during plate impact experiments to study the evolution of titanium during transformation. These high-rate data allow us to probe the mechanism and kinetics of phase transformations in new ways. Recent results will be presented and compared to post-mortem characterization of soft-recovered shocked specimens. Comparisons are then made with previous tests where material was shock-loaded and soft recovered for microstructural analysis. Together these techniques create a consistent picture of material behavior during the shock-induced α–ω phase transformation in titanium.

36 MATERIALS SCIENCE↗

Predicting Damages to Remainder Parcels in Right-of-Way Acquisitions for Expanding Transportation Infrastructure: Using a Truncated Finite-Mixture Model

Right-of-way acquisition is a critical component of transportation infrastructure development. Transportation infrastructure projects cannot proceed without proper right-of-way acquisition or may face significant delays. State Departments of Transportation frequently acquire parcels of land for roadway expansion projects. A majority of these acquisitions can be partial takings, referring to a portion of a parcel that is acquired. The remainder of the property usually suffers economic changes due to the partial acquisition, which can be calculated as damage percentages. The damage percentage represents the extent to which the remaining land or property value has been diminished due to the acquisition. It reflects the remaining property value percentage that may have been lost or compromised due to the acquisition. Here, this study aims to provide a robust model to estimate damage percentages to the remainder parcels that may help state Departments of Transportation appraisers make early predictions about the damages in cases involving partial takings. The research uses 509 appraisal reports from the Tennessee Department of Transportation to identify the key parcel attributes that influence the percentage of damages. Three regression models are developed: a linear regression model, a finite-mixture model (FMM), and a truncated FMM with two latent classes. The modeling results show that the truncated FMM with two classes outperforms the other models. To validate the models, actual sales data is collected and analyzed for 59 properties, and the results suggest that the model predictions are fairly accurate. A predictive tool is developed based on the models to help appraisers anticipate right-of-way damages under different scenarios and can provide early predictions about the damages.

42 ENGINEERING↗

Influence of sky radiance measurement errors on inversion-retrieved aerosol properties

Remote sensing of the atmospheric aerosol is a well-established technique that is currently used for routine monitoring of this atmospheric component, both from ground-based and satellite. The AERONET program, initiated in the 90's, is the most extended network and the data provided are currently used by a wide community of users for aerosol characterization, satellite and model validation and synergetic use with other instrumentation (lidar, in-situ, etc.). Aerosol properties are derived within the network from measurements made by ground-based Sun-sky scanning radiometers. Sky radiances are acquired in two geometries: almucantar and principal plane. Discrepancies in the products obtained following both geometries have been observed and the main aim of this work is to determine if they could be justified by measurement errors. Three systematic errors have been analyzed in order to quantify the effects on the inversion-derived aerosol properties: calibration, pointing accuracy and finite field of view. Simulations have shown that typical uncertainty in the analyzed quantities (5% in calibration, 0.2 Degree-Sign in pointing and 1.2 Degree-Sign field of view) yields to errors in the retrieved parameters that vary depending on the aerosol type and geometry. While calibration and pointing errors have relevant impact on the products, the finite field of view does not produce notable differences.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Initial conditions of radiative shock experiments

We performed experiments at the Omega Laser Facility to characterize the initial, laser-driven state of a radiative shock experiment. These experiments aimed to measure the shock breakout time from a thin, laser-irradiated Be disk. The data are then used to inform a range of valid model parameters, such as electron flux limiter and polytropic γ, used when simulating radiative shock experiments using radiation hydrodynamics codes. The characterization experiment and the radiative shock experiment use a laser irradiance of ∼7 × 10{sup 14} W cm{sup −2} to launch a shock in the Be disk. A velocity interferometer and a streaked optical pyrometer were used to infer the amount of time for the shock to move through the Be disk. The experimental results were compared with simulation results from the Hyades code, which can be used to model the initial conditions of a radiative shock system using the CRASH code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Intermittency in Hall-magnetohydrodynamics with a strong guide field

We present a detailed study of intermittency in the velocity and magnetic field fluctuations of compressible Hall-magnetohydrodynamic turbulence with an external guide field. To solve the equations numerically, a reduced model valid when a strong guide field is present is used. Different values for the ion skin depth are considered in the simulations. The resulting data are analyzed computing field increments in several directions perpendicular to the guide field, and building structure functions and probability density functions. In the magnetohydrodynamic limit, we recover the usual results with the magnetic field being more intermittent than the velocity field. In the presence of the Hall effect, field fluctuations at scales smaller than the ion skin depth show a substantial decrease in the level of intermittency, with close to monofractal scaling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nonlinear evolution of the magnetized Kelvin-Helmholtz instability: From fluid to kinetic modeling

The nonlinear evolution of collisionless plasmas is typically a multi-scale process, where the energy is injected at large, fluid scales and dissipated at small, kinetic scales. Accurately modelling the global evolution requires to take into account the main micro-scale physical processes of interest. This is why comparison of different plasma models is today an imperative task aiming at understanding cross-scale processes in plasmas. We report here the first comparative study of the evolution of a magnetized shear flow, through a variety of different plasma models by using magnetohydrodynamic (MHD), Hall-MHD, two-fluid, hybrid kinetic, and full kinetic codes. Kinetic relaxation effects are discussed to emphasize the need for kinetic equilibriums to study the dynamics of collisionless plasmas in non trivial configurations. Discrepancies between models are studied both in the linear and in the nonlinear regime of the magnetized Kelvin-Helmholtz instability, to highlight the effects of small scale processes on the nonlinear evolution of collisionless plasmas. We illustrate how the evolution of a magnetized shear flow depends on the relative orientation of the fluid vorticity with respect to the magnetic field direction during the linear evolution when kinetic effects are taken into account. Even if we found that small scale processes differ between the different models, we show that the feedback from small, kinetic scales to large, fluid scales is negligible in the nonlinear regime. This study shows that the kinetic modeling validates the use of a fluid approach at large scales, which encourages the development and use of fluid codes to study the nonlinear evolution of magnetized fluid flows, even in the collisionless regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗