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DOE OSTI2021

Multi-objective parametrization of interatomic potentials for large deformation pathways and fracture of two-dimensional materials

Abstract This investigation presents a generally applicable framework for parameterizing interatomic potentials to accurately capture large deformation pathways. It incorporates a multi-objective genetic algorithm, training and screening property sets, and correlation and principal component analyses. The framework enables iterative definition of properties in the training and screening sets, guided by correlation relationships between properties, aiming to achieve optimal parametrizations for properties of interest. Specifically, the performance of increasingly complex potentials, Buckingham, Stillinger-Weber, Tersoff, and modified reactive empirical bond-order potentials are compared. Using MoSe 2 as a case study, we demonstrate good reproducibility of training/screening properties and superior transferability. For MoSe 2 , the best performance is achieved using the Tersoff potential, which is ascribed to its apparent higher flexibility embedded in its functional form. These results should facilitate the selection and parametrization of interatomic potentials for exploring mechanical and phononic properties of a large library of two-dimensional and bulk materials.

Zhang, Xu↗

DOE OSTI2025

Support modification by phosphonic acid ligands controls ethylene hydroformylation on single-atom rhodium sites

To investigate the ability of surface-bound ligands to control activity toward ethylene hydroformylation, we modified site-isolated Rh 1 /TiO 2 with a series of substituted benzyl phosphonic acids. We found that modification of the support by phosphonic acids reduced break-in times for hydroformylation by 4× and increased absolute hydroformylation activity by up to 18× compared to unmodified catalyst at 150 °C. All functionalized catalysts improved hydroformylation activity by at least 9× and improved selectivity by between 7× and 60× relative to the unmodified catalyst. Carbon monoxide probe–molecule spectroscopy indicated that the enhancements in activity among modified samples were due to changes in the local environment of the active Rh site. Specifically, the bite angle of adsorbed carbon monoxide, as determined from infrared spectra, correlated with hydroformylation activity. These findings demonstrate that Rh 1 active sites are highly sensitive to modification of the support with organic ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Binding Sites for Acylated Trehalose Analogs of Glycolipid Ligands on an Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle

The macrophage receptor mincle binds to trehalose dimycolate on the surface of Mycobacterium tuberculosis. Signaling initiated by this interaction leads to cytokine production, which underlies the ability of mycobacteria to evade the immune system and also to function as adjuvants. In previous work the mechanism for binding of the sugar headgroup of trehalose dimycolate to mincle has been elucidated, but the basis for enhanced binding to glycolipid ligands, in which hydrophobic substituents are attached to the 6-hydroxyl groups, has been the subject of speculation. In the work reported here, the interaction of trehalose derivatives with bovine mincle has been probed with a series of synthetic mimics of trehalose dimycolate in binding assays, in structural studies by x-ray crystallography, and by site-directed mutagenesis. Binding studies reveal that, rather than reflecting specific structural preference, the apparent affinity of mincle for ligands with hydrophobic substituents correlates with their overall size. Structural and mutagenesis analysis provides evidence for interaction of the hydrophobic substituents with multiple different portions of the surface of mincle and confirms the presence of three Ca 2+ -binding sites. The structure of an extended portion of the extracellular domain of mincle, beyond the minimal C-type carbohydrate recognition domain, also constrains the way the binding domains may interact on the surface of macrophages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Modelling individual variability in growth of bull trout in the Walla Walla River Basin using a hierarchical von Bertalanffy growth model

Abstract We examined growth in length of fluvial bull trout ( Salvelinus confluentus ) in the Walla Walla River Basin, Washington and Oregon. Our objectives were to quantify individual variability in growth; examine growth within and among years, life history forms, life stages and sexes; and estimate von Bertalanffy growth parameters. Individual variability was evaluated by modelling asymptotic length ( L ∞ ) and the growth coefficient ( k ) as random variables. All models were fit with Bayesian methods and were evaluated for fit by the deviance information criterion. By incorporating individual variability, population‐level estimates of L ∞ and k appeared appropriate and estimated growth trajectories for specific bull trout fit individual observed patterns in growth. Growth trajectories and positive correlation between individual estimates of L ∞ and k suggest that some individuals grow at a faster rate and reach a larger maximum size than other individuals and those differences are maintained throughout life. Selected models suggest that fluvial migrants have higher estimates of L ∞ and k than residents, but there were only slight differences in parameter estimates among migrants from two adjacent spawning populations in the Walla Walla River Basin, as well as between males and females. Growth rates increased for fluvial migrants after subadult emigration. Individual variability in growth is consistent with the life history diversity assumed essential for bull trout population persistence. Quantifying this variability is important for modelling population dynamics and viability to conserve this threatened species.

Harris, Julianne E.↗

DOE OSTI2026

Endophyte‐induced systemic spatial reprogramming of metabolism in Populus trichocarpa roots under drought

Beneficial, facultative endophytes help plants thrive in challenging environments by altering their host's metabolism, but how these cellular scale metabolic changes propagate to the systems biology scale is unknown. In this work, we employed a high-resolution chemical imaging approach to map metabolic changes at the Populus trichocarpa root-zone and cell-type levels combined with machine learning (ML) models to identify root metabolites and exudates that have predictive power over treatment class. We found that a nine-strain consortium of beneficial endophytes differentially altered the metabolome of droughted root tissues in a manner specific to cell type and root zone, with endophyte abundance showing a clear correlation to individual metabolites. Our study demonstrates that integrating spatial metabolomics with ML can reveal localized metabolic patterns linked to root–microbe interactions and generate novel hypotheses about underlying biological mechanisms.

Drought↗

DOE OSTI2023

A new class of antibodies that overcomes a steric barrier to cross-group neutralization of influenza viruses

Antibody titers that inhibit the influenza virus hemagglutinin (HA) from engaging its receptor are the accepted correlate of protection from infection. Many potent antibodies with broad, intra-subtype specificity bind HA at the receptor binding site (RBS). One barrier to broad H1-H3 cross-subtype neutralization is an insertion (133a) between positions 133 and 134 on the rim of the H1 HA RBS. We describe here a class of antibodies that overcomes this barrier. These genetically unrestricted antibodies are abundant in the human B cell memory compartment. Analysis of the affinities of selected members of this class for historical H1 and H3 isolates suggest that they were elicited by H3 exposure and broadened or diverted by later exposure(s) to H1 HA. RBS mutations in egg-adapted vaccine strains cause the new H1 specificity of these antibodies to depend on the egg adaptation. The results suggest that suitable immunogens might elicit 133a-independent, H1-H3 cross neutralization by RBS-directed antibodies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Predicting departure from nucleate boiling with advanced data- and physics-driven approaches

The subcooled and low-quality saturated flow boiling critical heat flux (CHF) corresponding to the departure from nucleate boiling (DNB) is one of the major limiting factors in the design and operation of pressurized water reactors (PWRs). Due to lack of agreement on its physical mechanisms, development of an accurate DNB-type CHF model has been elusive. The various steady-state (SS) predictive tools that have been proposed can be grouped into two categories: (1) data-driven methods—namely best-fit empirical correlations and look-up tables that result in relatively good agreement with specific experimental datasets but often fail to extend beyond their ranges of validity, and (2) the physics-based mechanistic models that rely on reasonable yet limited understanding of the underlying physics and apply constitutive relations to close the conservation equations. On one hand, with recent advances in computational capabilities and optimization techniques, machine learning (ML)-based methods constitute an alternative and a more advanced, data-driven approach. With enough data, they can be particularly useful in engineering fields where the physical phenomena are complex and challenging to model. On the other hand, a state-of-the-art physics-driven approach would not only provide more accurate prediction of SS CHF, but it would also help better understand and model transient applications. The data-driven regression models use deep feed-forward neural networks (NNs) and random forests to cross-validate with 1,865 CHF test cases, covering a wide range of flow conditions and channel geometries. The best-estimate ML-based predictors compare favorably with the widely used look-up table for annulus and plate, and sensitivity analysis has confirmed their effectiveness. The key advantage of ML-based methods is their online extensibility of applicability domain. The proposed physics-driven approach combines key assumptions and parameters in the relatively well-accepted theories of liquid sublayer dryout and near-wall bubble crowding. A more realistic understanding of local mechanisms has been modeled. The new model has been optimized and validated against 1,439 tube data, and it shows considerably improved performance when compared to a recent mechanistic model, demonstrating unbiased close agreement with measurements over a wide range of operating conditions. Future work will extend the improved physics-driven model to non-tube geometry applications and will couple the model with ML via a hybrid approach. The mechanistic SS work will also serve to improve understanding and to model transient CHF scenarios.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Domain decomposition efforts in Chroma

Multilevel integration is a technique used in lattice quantum chromodynamics (LQCD) simulations, where the correlation functions are decomposed into factors that depend only on fields localized within specific lattice subdomains. The approach significantly improves the efficiency of the calculations because the factors can be independently integrated. The main challenge in implementing multilevel integration is that the standard formulation of the LQCD action is not local in the presence of fermions. However, past studies have shown that approximations of the quark propagator and the fermionic determinant, which depend on the gauge fields within specific subdomains, can still be effective. We will present the current progress in supporting domain decomposition within the Chroma software, which is necessary for implementing multilevel integration approaches. Most of the efforts have focused on extending the Chroma code base to efficiently manipulate subdomains for lattice fields and operators, as well as performing inversions and eigendecompositions within these domains.

Alcalde, Eloy Romero↗

DOE OSTI2026

Roll-to-Roll Manufacturing of Solid Oxide Fuel Cells

The overall goal of this project is to develop a high-volume electrode electrolyte assembly (EEA) production capability to significantly increase throughput of solid oxide fuel cell (SOFC) manufacturing and reduce the cost while maintaining the same level of performance. Specifically, four approaches will be adopted: 1) optimization of the lamination process and correlation of the EEA properties and performance with the lamination conditions; 2) scale up of the lamination process and demonstration of >10 ft of EEA; 3) further increase of the EEA throughput via slot-die coating and demonstration of > 5 m/min in coating the thick anode layer; and 4) minimization of the anode thickness to reduce material cost.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2022

Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s

Passive transfer of monoclonal antibodies (mAbs) of human origin into Non-Human Primates (NHPs), especially those which function predominantly by a Fc-effector mechanism, requires an a priori preparation step, in which the human mAb is reengineered to an equivalent NHP IgG subclass. This can be achieved by changing both the Fc and Fab sequence while simultaneously maintaining the epitope specificity of the parent antibody. This Ab reengineering process, referred to as rhesusization, can be challenging because the simple grafting of the complementarity determining regions (CDRs) into an NHP IgG subclass may impact the functionality of the mAb. Here we describe the successful rhesusization of a set of human mAbs targeting HIV-1 envelope (Env) epitopes involved in potent Fc-effector function against the virus. This set includes a mAb targeting a linear gp120 V1V2 epitope isolated from a RV144 vaccinee, a gp120 conformational epitope within the Cluster A region isolated from a RV305 vaccinated individual, and a linear gp41 epitope within the immunodominant Cys-loop region commonly targeted by most HIV-1 infected individuals. Structural analyses confirm that the rhesusized variants bind their respective Env antigens with almost identical specificity preserving epitope footprints and most antigen-Fab atomic contacts with constant regions folded as in control RM IgG1s. In addition, functional analyses confirm preservation of the Fc effector function of the rhesusized mAbs including the ability to mediate Antibody Dependent Cell-mediated Cytotoxicity (ADCC) and antibody dependent cellular phagocytosis by monocytes (ADCP) and neutrophils (ADNP) with potencies comparable to native macaque antibodies of similar specificity. While the antibodies chosen here are relevant for the examination of the correlates of protection in HIV-1 vaccine trials, the methods used are generally applicable to antibodies for other purposes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome

The human gut microbiome, which develops and stabilizes during the early stages of infant life, plays an essential role in host health through the production of metabolic resources and the stimulation and training of the immune system. To study colonization and community functional dynamics of the microbiota based on responses to host immune processes during the normal and dysbiotic establishment of the gut, metaproteomics was conducted on 91 fecal samples collected over the first 90 days of life from 17 hospitalized premature infants. Microbial responses to antibiotic administration and host-imposed metal bactericidal control correlated with community assembly and resiliency of microbes in the developing preterm gut. Specifically, proteins related to antibiotic resistance and metal homeostasis mechanisms were predominant in persisting members in the infant gut environment over the first several weeks of life. Overall, this metaproteomics study provides a unique approach to examine the temporal expansion and resilience of microbial colonization, as it allows simultaneous examination of both host and microbial metabolic activities. Understanding the interplay between host and microbes may elucidate the microbiome’s potential immunomodulatory roles relevant to necrotizing enterocolitis and other dysbiotic conditions in preterm infants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Full-core high-burnup BWR LOCA fuel performance analysis and FFRD susceptibility

The susceptibility of the boiling water reactor (BWR) Limerick Unit 1 to fuel fragmentation, relocation, and dispersal during a postulated large-break loss-of-coolant accident (LBLOCA) was calculated using a multiphysics framework. The simulations include full-core, rod-resolved neutronic, thermal hydraulic, and fuel performance models using the VERA, TRACE, and BISON codes. This work focused on the transient BISON simulations, which include both the normal operation and LBLOCA periods in the same simulations. Cladding integrity was assessed using two correlations that are included with BISON. make page break Several new BWR-specific features were recently added to BISON. This work represents the first time these features have been included in a core-scale set of simulations. This study hence evaluates the performance of these new models for an operating reactor with realistic operating conditions. Simulation results showed that cladding integrity was maintained (i.e., no rods burst). Finally, future work to improve BWR and PWR predictions using this framework is suggested.

BISON↗

DOE OSTI2021

Efficacy of Hair Total Mercury Content as a Biomarker of Methylmercury Exposure to Communities in the Area of Artisanal and Small-Scale Gold Mining in Madre de Dios, Peru

Total mercury content (THg) in hair is an accepted biomarker for chronic dietary methylmercury (MeHg) exposure. In artisanal and small-scale gold mining (ASGM) communities, the validity of this biomarker is questioned because of the potential for contamination from inorganic mercury. As mining communities may have both inorganic and organic mercury exposures, the efficacy of the hair-THg biomarker needs to be evaluated, particularly as nations begin population exposure assessments under their commitments to the Minamata Convention. We sought to validate the efficacy of hair THg for public health monitoring of MeHg exposures for populations living in ASGM communities. We quantified both THg and MeHg contents in hair from a representative subset of participants (N = 287) in a large, population-level mercury exposure assessment in the ASGM region in Madre de Dios (MDD), Peru. We compared population MeHg-THg correlations and %MeHg values with demographic variables including community location, sex, occupation, and nativity. We observed that hair MeHg-THg correlations were high (r > 0.7) for all communities, regardless of location or nativity. Specifically, for individuals within ASGM communities, 81% (121 of 150 total) had hair THg predominantly in the form of MeHg (i.e., >66% of THg) and reflective of dietary exposure to mercury. Furthermore, for individuals with hair THg exceeding the U.S. EPA threshold (1.0 μg/g), 88 out of 106 (83%) had MeHg as the predominant form. As a result, had urine THg solely been used for mercury exposure monitoring, approximately 59% of the ASGM population would have been misclassified as having low mercury exposure. Our results support the use of hair THg for monitoring of MeHg exposure of populations in ASGM settings where alternative biomarkers of MeHg exposure are not feasible.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2023

First-principles-integrated Study of Blazar Synchrotron Radiation and Polarization Signatures from Magnetic Turbulence

Blazar emission is dominated by nonthermal radiation processes that are highly variable across the entire electromagnetic spectrum. Turbulence, which can be a major source of nonthermal particle acceleration, can widely exist in the blazar emission region. The Turbulent Extreme Multi-Zone (TEMZ) model has been used to describe turbulent radiation signatures. Recent particle-in-cell (PIC) simulations have also revealed the stochastic nature of the turbulent emission region and particle acceleration therein. However, radiation signatures have not been systematically studied via first-principles-integrated simulations. In this paper, we perform combined PIC and polarized radiative transfer simulations to study synchrotron emission from magnetic turbulence in the blazar emission region. We find that the multiwavelength flux and polarization are generally characterized by stochastic patterns. Specifically, the variability timescale and average polarization degree (PD) are governed by the correlation length of the turbulence. Interestingly, magnetic turbulence can result in polarization angle swings with arbitrary amplitudes and duration, in either direction, that are not associated with changes in flux or PD. Surprisingly, these swings, which are stochastic in nature, can appear either bumpy or smooth, although large-amplitude swings (>180°) are very rare, as expected. Our radiation and polarization signatures from first-principles-integrated simulations are consistent with the TEMZ model, except that in the latter, there is a weak correlation, with zero lag, between flux and degree of polarization.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics

Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes than with “narrow” functions in which specific microorganisms specialize. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with broad and narrow functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five broad and the five narrow functions that we chose. Our results revealed that, compared with the five broad functions, soil microbes capable of performing the five narrow functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in narrow functions. Co-occurrence networks indicated that microorganisms conducting broad functions were positively related, but microbes specializing in narrow functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between broad and narrow functions in soil microbes, as the association of functional diversity with taxonomy was greater in the five narrow than in the five broad functions.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1973

Significant techniques in the processing and interpretation of ERTS-1 data

The discipline oriented investigations underway at the Johnson Space Center (JSC) using ERTS-1 data provide an appropriate framework for the systematic evaluation of the various elements comprising a prototype multispectral data processing and analysis system. In particular such a system may be thought of as the integration of: (1) a preprocessing subsystem; (2) a spectral clustering subsystem, (3) a correlation and classification subsystem; (4) mensuration subsystem; and (5) an information management subsystem. Specific elements of this system are already operational at JSC. It is in the context of this system that technique development and application is being pursued at JSC. Aircraft, ERTS and EREP data will be utilized to refine the subsystem elements for each of the data acquisition systems or system combinations that are optimally suited for a specific Earth Resources application. The techniques reported are those that have been developed to date during the utilization of ERTS-1 data in this processing and analysis system.

Cousin, S. B.↗

NASA NTRS1975

Application of ERTS images and image processing to regional geologic problems and geologic mapping in northern Arizona

The author has identified the following significant results. Computer image processing was shown to be both valuable and necessary in the extraction of the proper subset of the 200 million bits of information in an ERTS image to be applied to a specific problem. Spectral reflectivity information obtained from the four MSS bands can be correlated with in situ spectral reflectance measurements after path radiance effects have been removed and a proper normalization has been made. A detailed map of the major fault systems in a 90,000 sq km area in northern Arizona was compiled from high altitude photographs and pre-existing published and unpublished map data. With the use of ERTS images, three major fault systems, the Sinyala, Bright Angel, and Mesa Butte, were identified and their full extent measured. A byproduct of the regional studies was the identification of possible sources of shallow ground water, a scarce commodity in these regions.

Goetz, A. F. H.↗