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At least 595 records · Page 33

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↗

TRUST-EABM Contact Thermal Conductance (CTC) Report

(U) Single Feature Testbeds to Reduce Uncertainty in Simulations and Tests [3] provided an overview for the need of experiments, with accompanying models and simulations, specifically designed to reduce uncertainties and build confidence in complex testing and analysis applications. The Contact Thermal Conductance (CTC) testbed is a joint effort between W-13 (formerly E-13) and MST-8. The objective of this study was to design a testbed, with accompanying finite element models, to quantify, reduce, and propagate measurement uncertainties in contact thermal conductance measurements between two mating components in WR-like thermal environments. The knowledge gained through this simplified experiment would educate more complex assessments and interaction conditions with WR-like materials and geometries.

42 ENGINEERING↗

High-Speed Diagnostic and Simulation Capabilities for Reacting Hypersonic Reentry Flows (LDRD Final Report)

High-enthalpy hypersonic flight represents an application space of significant concern within the current national-security landscape. The hypersonic environment is characterized by high-speed compressible fluid mechanics and complex reacting flow physics, which may present both thermal and chemical nonequilibrium effects. We report on the results of a three-year LDRD effort, funded by the Engineering Sciences Research Foundation (ESRF) investment area, which has been focused on the development and deployment of new high-speed thermochemical diagnostics capabilities for measurements in the high-enthalpy hypersonic environment posed by Sandia's free-piston shock tunnel. The project has additionally sponsored model development efforts, which have added thermal nonequilibrium modeling capabilities to Sandia codes for subsequent design of many of our shock-tunnel experiments. We have cultivated high-speed, chemically specific, laser-diagnostic approaches that are uniquely co-located with Sandia's high-enthalpy hypersonic test facilities. These tools include picosecond and nanosecond coherent anti-Stokes Raman scattering at 100-kHz rates for time-resolved thermometry, including thermal nonequilibrium conditions, and 100-kHz planar laser-induced fluorescence of nitric oxide for chemically specific imaging and velocimetry. Key results from this LDRD project have been documented in a number of journal submissions and conference proceedings, which are cited here. The body of this report is, therefore, concise and summarizes the key results of the project. The reader is directed toward these reference materials and appendices for more detailed discussions of the project results and findings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Light- and Chemical-Doping-Induced Magnetic Behavior of Eu Molecular Systems

Variable temperature electron paramagnetic resonance (VT-EPR) was used to investigate the role of the environment and oxidation states of several coordinated Eu compounds. We find that while Eu(III) chelating complexes are diamagnetic, simple chemical reduction results in the formation of paramagnetic species. In agreement with the distorted D 3h symmetry of Eu molecular complexes investigated in this study, the EPR spectrum of reduced complexes showed axially symmetric signals (g ⊥ = 2.001 and g ∥ = 1.994) that were successfully simulated with two Eu isotopes with nuclear spin 5/2 ( 151 Eu and 153 Eu with 48% and 52% natural abundance, respectively) and nuclear g-factors 151 Eu/ 153 Eu = 2.27. Illumination of water-soluble complex Eu(dipic) 3 at 4 K led to the ligand-to-metal charge transfer (LMCT) that resulted in the formation of Eu(II) in a rhombic environment (g x = 2.006, g y = 1.995, g z = 1.988). The existence of LMCT affects the luminescence of Eu(dipic) 3 , and pre-reduction of the complex to Eu(II)(dipic) 3 reversibly reduces red luminescence with the appearance of a weak CT blue luminescence. Furthermore, encapsulation of a large portion of the dipic ligand with Cucurbit[7]uril, a pumpkin-shaped macrocycle, inhibited ligand-to-metal charge transfer, preventing the formation of Eu(II) upon illumination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In situ temperature profile measurements with high-energy X-rays as a probe of optical floating zone crystal growth environment

The ability of optical floating zone (OFZ) furnaces to rapidly produce large single crystals of complex emerging materials has had a transformative effect on many scientific fields that require samples of this type. However, the crystal growth process within the OFZ furnace is not well understood owing to the challenges involved in monitoring the high-temperature crystal growth process. Novel beamline-compatible optical furnaces that approximate the inhomogeneous growth environment within an OFZ furnace have been fabricated and tested in high-energy synchrotron beamlines. In this paper, it is demonstrated that temperature profiles can be effectively extracted from powder diffraction data collected on polycrystalline ceramic rods heated at their tip. Furthermore, these measured temperature profiles can be accurately reproduced using a heat-transfer model that accounts for solid-state thermal conduction, partial sample lamp power absorption, convective air cooling and radiative cooling, allowing key thermal parameters such as thermal conductivity to be extracted from experimental data.

36 MATERIALS SCIENCE↗

Evolution of lithium ordering with (de)-lithiation in β-LiVOPO 4 : insights through solid-state NMR and first principles DFT calculations

The lithium-ion battery cathode material β-VOPO 4 is capable of intercalating more than one Li ion per transition metal ion due to the accessibility of both the V 5+ /V 4+ and V 4+ /V 3+ redox couples at ~4.5 V and ~2.3 V vs. Li, respectively, giving a theoretical capacity greater than ~300 mA h g -1 . The ability to perform full and reversible two Li-ion intercalation in this material, however, has been a matter of debate and the poor crystallinity of the fully lithiated phase has thus far precluded its complete structural characterisation by conventional diffraction-based methods. In this work, 7 Li and 31 P NMR spectroscopy, in combination with first principles DFT calculations, indicate that chemical lithiation results in a single phase β-Li 2 VOPO 4 exhibiting a complex Li ordering scheme with lithium ions occupying multiple disordered environments. 2D NMR 7 Li correlation experiments were used to deduce the most likely Li ordering for the β-Li 2 VOPO 4 phase from amongst several DFT optimised structures. In contrast, electrochemically lithiated β-Li 2- x VOPO 4 discharged to 1.6 V exhibits, in addition to β-Li 2 VOPO 4 , a β-Li 1.5 VOPO 4 phase. Additionally, the existence of β-Li 1.5 VOPO 4 is not reflected in the flat galvanostatic charge and discharge curves nor is evident from diffraction-based methods due to the very close structural similarity between the β-Li 1.5 VOPO 4 phase and β-Li 2 VOPO 4 phases. We demonstrate that solid state NMR spectroscopy, in combination with DFT results, provides a powerful tool for identifying intermediate states formed during charge/discharge of these complex phosphates as these phases can be distinguished from the end member phases primarily by the nature of the lithium ordering.

25 ENERGY STORAGE↗

Adsorption of Neodymium, Dysprosium, and Ytterbium to Goethite under Varying Aqueous Chemistry Conditions

The adsorption of rare earth elements (REEs) to iron oxides can regulate the mobility of REEs in the environment and is heavily influenced by water chemistry. This study utilized batch experiments to examine the adsorption of Nd, Dy, and Yb to goethite under varying pH, electrolyte (type and concentration), and concentrations of dissolved inorganic carbon and citrate. REE adsorption was strongly influenced by pH, with an increase from essentially no adsorption at pH 3.0 to nearly complete adsorption at pH 6.5 and higher. Citrate enhanced the adsorption of REEs at low pH (<5.0), likely by forming goethite-REE-citrate ternary surface complexes. However, citrate inhibited the adsorption of REEs at higher pH (>5.0) by forming aqueous REE-citrate complexes. Ionic strength had a small influence on REE adsorption, and the presence of dissolved inorganic carbon had no discernible effect. Equilibrium adsorption was interpreted with a triple-layer surface complexation model (SCM). The selection of surface complexation reactions was guided by extended X-ray absorption fine structure spectra. An SCM with a single bidentate inner-sphere surface complexation reaction for Nd and two inner-sphere surface complexation reactions (one monodentate and one bidentate reaction) for Dy and Yb effectively simulated adsorption across a broad range of conditions in the absence of citrate. Accounting for the effects of citrate on REE adsorption required the addition of up to two ternary REE-citrate-goethite surface complexes. The SCM can enable predictions of REE transport in subsurface environments that have goethite as an important adsorbent mineral. Furthermore, this predictive capability could contribute to identifying potential REE sources and facilitating efficient extraction of REEs.

58 GEOSCIENCES↗

Influence of americium complexation on the radiation-induced chemical reactivity of sulfophenyl bistriazinyl pyridine (SO 3 -Ph-BTP) towards the nitrate radical

Sulfophenyl bistriazinyl pyridine (SO 3 -Ph-BTP) is a hydrophilic organic ligand used to separate actinides and lanthanides. Dose accumulation and time-resolved studies have previously provided insight into the radiolytic stability and degradation pathways of SO 3 -Ph-BTP in reprocessing environments, but no study has yet addressed the impact of minor actinide complexation on the radiation chemistry of this ligand. To begin to fill this knowledge gap, a systematic, time-resolved study exploring the reactivity of the nitrate radical (NO 3 • ) with SO 3 -Ph-BTP in the presence of trivalent americium, Am(III), has been conducted, which demonstrates enhanced reactivity (an order of magnitude faster) upon metal complexation.

38 - RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCL↗

Machine Learning in Environmental Chemistry: Application to Surface Complexation Modeling

Environmental chemistry – or biogeochemistry – is the scientific discipline typically invoked when examining and quantifying groundwater or surface water contamination, and nutrient cycling in the environment. Over the last three decades, there have been significant advances in mechanistic model development to describe and predict these complex biogeochemical processes. In particular, surface complexation models (SCMs) have been developed to describe the rock/soil surface reactions of metals and radionuclides, and their partitioning between various mobile species in the aqueous phase or immobile species sorbed on solid surfaces. Often represented by a simplified linear isotherm constant – Kd – in reactive transport models, these reactions play a critical role in many environmental science applications; particularly in contamination risk assessments and nuclear waste disposal performance assessments. In the past several decades, efforts by various institutions across the world have focused on developing SCMs based on datasets from laboratory measurements, including the identification of key parameters such as equilibrium constants.

54 ENVIRONMENTAL SCIENCES↗

The Indian Ocean, its supra-subduction history, and implications for ophiolites

We report Ophiolite complexes represent fragments of ocean crust and mantle formed at spreading centers and emplaced on land. The setting of their origin, whether at mid-ocean ridges, back-arc basins, or forearc basins has been debated. Geochemical classification of many ophiolite extrusive rocks reflect an approach interpreting their tectonic environment as the same as rocks with similar compositions formed in various modern oceanic settings. This approach has pointed to the formation of many ophiolitic extrusive rocks in a supra-subduction zone (SSZ) environment. Paradoxically, structural and stratigraphic evidence suggests that many apparent SSZ-produced ophiolite complexes are more consistent with mid-ocean ridge settings. Compositions of lavas in the southeastern Indian Ocean resemble those of modern SSZ environments and SSZ ophiolites, although Indian Ocean lavas clearly formed in a mid-ocean ridge setting. These facts suggest that an interpretation of the tectonic environment of ophiolite formation based solely on their geochemistry may be unwarranted. New seismic images revealing extensive Mesozoic subduction zones beneath the southern Indian Ocean provide one mechanism to explain this apparent paradox. Cenozoic mid-ocean-ridge–derived ocean floor throughout the southern Indian Ocean apparently formed above former sites of subduction. Compositional remnants of previously subducted mantle in the upper mantle were involved in generation of mid-ocean ridge lavas. The concept of historical contingency may help resolve the ambiguity on understanding the environment of origin of ophiolites. Many ophiolites with “SSZ” compositions may have formed in a mid-ocean ridge setting such as the southeastern Indian Ocean.

58 GEOSCIENCES↗

A high-performance lung-inspired ceramic 3D-printed heat exchanger for high-temperature energy-efficient systems

The thermal-to-electric conversion efficiency of next-generation supercritical carbon dioxide and concentrated solar power plants is significantly augmented by operating at temperatures exceeding 1000 °C if durable, compact, high-temperature heat exchangers (HXs) are developed. Whereas metal 3D-printed HXs fail to operate under extreme temperature conditions, ceramic 3D-printed HXs are deemed promising candidates for high-temperature, highly oxidizing environments. Ceramic 3D-printed HXs, however, exhibit a high gas permeability issue through hot and cold separating walls due to an excessive non-volatile photopolymer content utilized. Here, in this work, a novel leak-free lung-inspired ceramic 3D-printed HX employing a highly complex heat transfer topology is introduced for high-temperature energy-efficient systems. The high permeability issue of ceramic 3D-printed HXs is fully eliminated through a uniform zinc-based coating. It was determined that the effective thermal conductivity of the sintered ceramic heat exchangers is affected by the coated layer. The high-temperature thermal and hydraulic characteristics of the lung-inspired ceramic 3D-printed HX are comprehensively examined and compared against a millichannel 3D-printed HX module. Experimental results indicated that the lung-inspired 3D-printed ceramic HX significantly outperforms its millichannel counterpart. The lung-inspired HX shows a volume-based power density of 8.2 MW/m3 at a hot-side inlet air temperature of 700°C, a 71 % improvement compared with that of the millichannel HX. More importantly, the higher thermal duty of the lung-inspired 3D-printed HX is realized at a lower normalized pressure drop penalty of 510 Pa/W, 22 % lower than that of the millichannel ceramic HX. This study accelerates the advancement of high-performance ceramic 3D-printed HXs with complex topologies for high-temperature energy-efficient systems and/or corrosive environments.

42 ENGINEERING↗

Similarity Metric for Data Optimization and Efficient Training of Reactive Machine Learning Force Fields for Hydrocarbon Radiolysis

Radiolysis is a common approach to sterilize polymers, chemically modify them for upcycling, and accelerate their decomposition for recycling purposes. Reactive molecular dynamics (MD) simulations provide a powerful tool to generate atomic-level trajectories of the reactive processes and quantify radiolytic chemical degradation pathways. For this, machine learning (ML) surrogate models for reactive force fields with quantum mechanical accuracy are now widely used, which require ML training data sets that can provide information on atomic environments for target chemical systems. However, radiolysis chemistry can be highly complex and diverse, which poses significant challenges for generating training data to parametrize ML models. In this regard, we developed a method for optimizing the training data set using a cosine similarity metric to help guide training set selection for radiolysis of polyethylene, a model hydrocarbon polymer, as well as to enhance the transferability of our reactive ML force field (MLFF) to a variety of molecular and polymeric systems. Our approach performs atom-by-atom comparisons between local atomic environments to pinpoint important data points associated with rare and localized events, such as radiolysis damage within structures. We apply this approach to train the Chebyshev Interaction Model for Efficient Simulation (ChIMES) MLFF model, which expresses the atomic interaction potentials in terms of linear combinations of many-body Chebyshev polynomials. We first show that our method can reduce our training set size by ∼70% while improving overall accuracy compared to more standard MD model fitting approaches. We then validate our optimum model against diverse hydrocarbon simulation data, including simple alkanes and systems with unsaturated carbon bonds, over a wide range of thermodynamic conditions. Finally, we use our ChIMES model to perform MD simulations of radiolytic damage with large-scale systems that help avoid system size effects. Overall, our approach yields an MD force field that retains most of the accuracy of the underlying quantum method while yielding many orders of improvement in computational efficiency. In conclusion, our efforts will have impact on future hydrocarbon polymer radiolysis studies, where the chemical details of the polymer–radiation interactions can have a strong effect on the resulting products observed in experiments.

Hydrocarbons↗

Adsorption of neodymium, dysprosium, and ytterbium to goethite under varying aqueous chemistry conditions [dataset]

The adsorption of rare earth elements (REEs) to iron oxides can regulate the mobility of REEs in the environment and is heavily influenced by water chemistry. This study utilized batch experiments to examine the adsorption of Nd, Dy, and Yb to goethite under varying pH, electrolyte (type and concentration), and concentrations of dissolved inorganic carbon and citrate. REE adsorption was strongly influenced by pH, with an increase from essentially no adsorption at pH 3.0 to nearly complete adsorption at pH 6.5 and higher. Citrate enhanced the adsorption of REEs at low pH (< 5.0), likely by forming goethite-REE-citrate ternary surface complexes. However, citrate inhibited the adsorption of REEs at higher pH (> 5.0) by forming aqueous REE-citrate complexes. Ionic strength had a small influence on REE adsorption, and the presence of dissolved inorganic carbon had no discernible effect. Equilibrium adsorption was interpreted with a triple layer surface complexation model (SCM). The selection of surface complexation reactions was guided by extended X-ray absorption fine structure spectra. A SCM with a single bidentate inner-sphere surface complexation reaction for Nd and two inner-sphere surface complexation reactions (one monodentate and one bidentate reaction) for Dy and Yb effectively simulated adsorption across a broad range of conditions in the absence of citrate. Accounting for the effects of citrate on REE adsorption required the addition of up to two ternary REE-citrate-goethite surface complexes. The SCM can enable predictions of REE transport in subsurface environments that have goethite as an important adsorbent mineral. This predictive capability could contribute to identifying potential REE sources and facilitating efficient extraction of REEs.

58 GEOSCIENCES↗

KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics

KRAS4a and KRAS4b are important regulators of signaling, and their interactions with the plasma membrane are dynamic and influenced by lipid composition. KRAS 4a and 4b have nearly identical globular domains but differ in their membrane-associated hyper variable region (HVR). The functional distinctions between these isoforms remain unclear, particularly with regards to their dependence on specific lipids and the membrane environment. Previous work showed that the membrane orientation of KRAS4b affects its ability to bind to RAF kinase RBDCRD and that the KRAS–RBDCRD complex adopts different poses on the membrane as well as influences the size and composition of the lipid environment. To model differences between KRAS 4a and 4b protein–lipid interactions, we extended the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to incorporate continuum simulations in the grand canonical ensemble, enabling sampling across macroscopic, coarse-grained, and all-atom resolutions. Using this framework, we systematically altered PIP2 concentrations, KRAS 4a versus 4b, and RAF RBDCRD complexation to assess impacts on membrane–protein interactions and dynamics. Our results reveal that reducing PIP2 shifts and broadens the membrane orientational preference of both KRAS 4b and 4a, with stronger effects on 4b HVR localization versus 4a. We demonstrate that with depletion of the strong negatively charged PIP2 lipid, the less charged phosphatidylserine replaces PIP2. Our findings highlight similarities and distinctions in the dynamics and lipid dependency of KRAS isoforms and suggest that ordering of the local lipid composition by HVRs is a shared property and key modulator of RAS-mediated signaling at the plasma membrane.

Biological and medical sciences↗

Overdestabilization vs Overstabilization in the Theoretical Analysis of f-Orbital Covalency

The complex nature of the f-orbital electronic structures and their interaction with the chemical environment pose significant computational challenges. Advanced computational techniques that variationally include scalar relativities and spin–orbit coupling directly at the molecular orbital level have been developed to address this complexity. Among these, variational relativistic multiconfigurational multireference methods stand out for their high accuracy and systematic improvement in studies of f-block complexes. Additionally, these advanced methods offer the potential for calibrating low-scaling electronic structure methods such as density functional theory. However, studies on the Cl K-edge X-ray absorption spectra of the [Ce(III)Cl 6 ] 3– and [Ce(IV)Cl 6 ] 2– complexes show that time-dependent density functional theory with approximate exchange–correlation kernels can lead to inaccuracies, resulting in an overstabilization of 4f orbitals and incorrect assessments of covalency. In contrast, approaches utilizing small active space wave function methods may understate the stability of these orbitals. The results herein demonstrate the need for large active space, multireference, and variational relativistic methods in studying f-block complexes.

chemical calculations↗

Spectroscopic Insight on Neodymium Solvation in Lithium Borohydride-Supported Electrolyte

Borohydride-based electrolytes have recently emerged as promising media for the electrodeposition of electropositive metals, including rare earth (RE) elements. While the presence of supporting alkali metal cations and RE counteranions provides essential electrochemical conductivity for achieving fast metal electrodeposition, interactions between the host ligand and solvated neodymium (Nd) complexes remain unclear. This study provides insights into the coordination structure of a concentrated and directly solvated Nd salt in a lithium borohydride-supported electrolyte. Our spectroscopic results indicate that the RE coordination environment is significantly influenced by the solvation mechanism, which can vary between metathesis and complexation pathways, primarily dictated by stoichiometric factors. Under dilute conditions, nearly complete metathesis of anions leads to a high coordination number for the host ligand (borohydride), consistent with the previously reported solvated Nd speciation in chlorine-free electrolytes. In contrast, concentrated dissolution of the Nd salt in the supported electrolyte is dominated by a complexation pathway featuring a Li-ion-paired complex with a low coordination number of the host ligand. Density functional theory (DFT) calculations indicated that the observed blue shift in the borohydride vibration was the result of an increase in electron density drawn into the terminal B–H interbond region from the hydride as the coordination changed from Li to Nd. In conjunction with DFT results, vibrational analyses allowed correlation of the experimental shifts associated with changes in Nd ligation and coordination spheres, further consolidating the prevalence of highly chloride-coordinated species under concentrated conditions. In conclusion, the outcomes of this work illuminate the distinctive and heterogeneous coordination structures that the electroactive RE species can adopt at high concentrations in lithium borohydride-supported electrolytes, as a key step to comprehend the reported metal electrodeposition performance in these media.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Site 300 Roadway Improvements - 834 Complex Soil Sampling and Analysis Plan

This Soil Sampling and Analysis Plan (SAP) was prepared by the Environmental Functional Area (EFA)/Technical Services Department (TSD) of the Environment, Safety & Health (ES&H) Directorate for the Project Management Office (PMO) for the proposed Roadway Improvements Project at the 834 Complex (project) (Figure 1). The purpose of the SAP is to describe the procedures for collection and analysis of environmental samples and evaluation of analytical data (chemical and radiological) to determine management options of excavated soil during project construction. This SAP follows criteria established in Lawrence Livermore National Laboratory’s (LLNL) Soils Screening and Management Plan (SSMP) (LLNL 2022), which was formalized in accordance with U.S. Environmental Protection Agency (EPA) guidance for developing Data Quality Objectives for environmental data (EPA 2006) and the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) guidance (U.S. NRC, U.S. EPA, U.S. DOE, and U.S. DOD 2000). The scope of this SAP is based on preliminary design information provided by PMO.

54 ENVIRONMENTAL SCIENCES↗