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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12

Factorization Machine‐Based Active Learning for Functional Materials Design with Optimal Initial Data

The optimization of functional materials is important to enhance their properties, but their complex geometries pose great challenges to optimization. Data-driven algorithms efficiently navigate such complex design spaces by learning relationships between material structures and performance metrics to discover high-performance functional materials. Surrogate-based active learning, continually improving its surrogate model by iteratively including high-quality data points, has emerged as a cost-effective data-driven approach. Furthermore, it can be coupled with quantum computing to enhance optimization processes, especially when paired with a special form of surrogate model (i.e., quadratic unconstrained binary optimization), formulated by factorization machine (FM). However, current practices often overlook the variability in design space sizes when determining the initial data size for optimization. In this work, we investigate the optimal initial data sizes required for efficient convergence across various design space sizes. By employing averaged piecewise linear regression, we identify initiation points where convergence begins, highlighting the crucial role of employing adequate initial data in achieving efficient optimization. These results contribute to the efficient optimization of functional materials by ensuring faster convergence and reducing computational costs in FM-based active learning.

active learning↗

Synthesis, aphicidal activity and conformation of novel insect kinin analogues as potential eco‐friendly insecticides

Abstract BACKGROUND The discovery of ecofriendly insecticides through a new strategy for aphid control is important because of the substantial resistance and unexpected eco‐toxicity to honeybees caused by traditional insecticides. The insect kinins, a class of multifunctional insect neuropeptides, are considered for potential application in pest control. In our previous work we developed several series of insect kinin analogues and found a promising lead II‐1 with good aphicidal activity. To seek further eco‐friendly aphicides, the optimization of II‐1 is carried out in this study. RESULTS Fifteen novel Yaa 3 modified analogues based on the lead II‐1 were synthesized. The aphicidal tests indicated that IV‐3 , IV‐5 and IV‐10 exhibited significant activity against the soybean aphid Aphis glycines with LC 50 values of 0.0029, 0.0072 and 0.0086 mmol L –1 , respectively, higher than that of lead II‐1 and the commercial Pymetrozine. The molecular modeling results showed that analogues II‐1 , IV‐3 , IV‐5 , IV‐7 and IV‐10 formed a β‐turn‐like conformation, while the conformation of analogues IV‐1 , IV‐2 and IV‐9 seemed to be linear. Some structural elements favorable for the activity were proposed based on the conformation‐activity relationship of the analogues. CONCLUSION Insect kinin analogues derived from lead II‐1 by modifying the hydrolysis site Yaa 3 with natural, sterically hindered α‐ and β‐amino acids showed great potential as eco‐friendly insecticides. Inspiringly, the most active analogue IV‐3 can be a candidate for further development. The β‐turn‐like conformation and the orientation of the aromatic rings of the side chain of Phe 2 and Trp 4 may be critical factors beneficial to activity. © 2019 Society of Chemical Industry

Zhang, Chuanliang↗

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Here, ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.

59 BASIC BIOLOGICAL SCIENCES↗

Control of light, spin and charge with chiral metal halide semiconductors

We report the relationship between the structural asymmetry and optoelectronic properties of functional materials is an active area of research. The movement of charges through an oriented chiral medium depends on the spin configuration of the charges, and such systems can be used to control spin populations without magnetic components - termed the chiral-induced spin selectivity (CISS) effect. CISS has mainly been studied in chiral organic molecules and their assemblies. Semiconductors are non-magnetic extended systems that allow for the control of charge transport, as well as the absorption and emission of light. Therefore, introducing chirality into semiconductors would enable control over charge, spin and light without magnetic components. Chiral metal halide semiconductors (MHSs) are hybrid organic-inorganic materials that combine the properties of small chiral organic molecules with those of extended inorganic semiconductors. Reports of CISS in chiral MHSs have resulted in breakthroughs in our understanding of CISS and in the realization of spin-dependent optoelectronic properties. This Review examines the fundamentals and applications of CISS in chiral MHSs. The structural diversity and key structure-property relationships, such as chiral transfer from the organic to the inorganic components, are summarized. With a focus on the underlying chemistry and physics, the control of spin, light and charge in these semiconductors is explored.

14 SOLAR ENERGY↗

Microstructural refinement of cement paste internally cured by polyacrylamide composite hydrogel particles containing silica fume and nanosilica

Supplementary cementitious materials were incorporated into hydrogel-based internal curing agents to improve the hydration, microstructure, and ultimately strength of internally cured high-performance cement paste. Polyacrylamide composite hydrogel particles containing amorphous silica – either silica fume or nanosilica – and two different polymer network crosslink densities were synthesized and incorporated into cement paste. The presence of silica and low crosslink density increased the absorption capacity of the particles in pore solution. Micrographs of internally cured paste indicated a significant improvement in hydrogel-related void-filling ability and an increase in void size for low crosslink density particles containing silica. Compressive strength and electrical resistivity increased at later ages for paste samples containing particles with higher silica dosage. The relationship between extent of hydration, void size, and void-filling activity was found to strongly influence the paste's long-term strength and is thus an important structure-property relationship to consider when selecting hydrogels for internal curing purposes.

36 MATERIALS SCIENCE↗

Regulating the Third Metal to Design and Engineer Multilayered NiFeM (M: Co, Mn, and Cu) Nanofoam Anode Catalysts for Anion-Exchange Membrane Water Electrolyzers

In this study, alkaline anion-exchange membrane water electrolyzers (AEMWEs) for green hydrogen production have received intensive attention due to their feasibility of using earth-abundant platinum group metal (PGM)-free catalysts. Herein, the third metal is incorporated into NiFe-based catalysts to regulate their electronic structures and morphologies, aiming to achieve sufficient oxygen evolution reaction (OER) activity and performance in AEMWEs. The ternary NiFeM (M: Cu, Co, or Mn) catalysts are featured with multiple layered structures and nanofoam network morphologies, consisting of highly OER-active amorphous Ni-rich oxide shells and electrically conductive metallic alloy cores. The physical and electronic perturbations to the NiFe induced by a third element lead to a fine-tuning of the redox ability of the metal sites at the reaction centers, which breaks the scaling relationship between OH* and O* intermediates at the reaction centers. Thus, the unique structural configuration and electronic regulation simultaneously benefit catalytic activity and performance improvements. These NiFeM nanofoam catalysts demonstrated promising anode performance in actual AEMWEs, comparable to the IrO 2 reference, especially at high current densities. Notably, using various electrolytes (e.g., KOH solution or pure water) for AEMWEs exhibited a different performance trend among studied NiFeM catalysts, likely due to dynamic changes of catalysts under various OER environments.

25 ENERGY STORAGE↗

Characterization of two distinct neutrophil serine protease–binding modes within a Staphylococcus aureus innate immune evasion protein family

Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure–function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10 -9 M) and of NE (on the order of 10 -10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct strain correlations at the single-atom level in three-dimensional core-shell interface structures

Abstract Nanomaterials with core-shell architectures are prominent examples of strain-engineered materials. The lattice mismatch between the core and shell materials can cause strong interface strain, which affects the surface structures. Therefore, surface functional properties such as catalytic activities can be designed by fine-tuning the misfit strain at the interface. To precisely control the core-shell effect, it is essential to understand how the surface and interface strains are related at the atomic scale. Here, we elucidate the surface-interface strain relations by determining the full 3D atomic structure of Pd@Pt core-shell nanoparticles at the single-atom level via atomic electron tomography. Full 3D displacement fields and strain profiles of core-shell nanoparticles were obtained, which revealed a direct correlation between the surface and interface strain. The strain distributions show a strong shape-dependent anisotropy, whose nature was further corroborated by molecular statics simulations. From the observed surface strains, the surface oxygen reduction reaction activities were predicted. These findings give a deep understanding of structure-property relationships in strain-engineerable core-shell systems, which can lead to direct control over the resulting catalytic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An active learning high-throughput microstructure calibration framework for solving inverse structure–process problems in materials informatics

Determining a process–structure–property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process–property linkage by bypassing the materials structure, or in the context of structure–property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process–structure linkage, which has a great implication in reverse engineering. In this paper, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization to exploit high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.

36 MATERIALS SCIENCE↗

Cold-cap structure in a slurry-fed electric melter

We report as glass batch is charged into an electric melter, a cold cap forms on the glass melt surface. Heat transfer to the cold cap from the molten glass below and the melter atmosphere above determines the melting rate. A mathematical model of the cold cap and the experimental kinetic data of the feed-to-glass conversion that were collected for several simulated low-activity and high-level waste melter feeds allowed us to develop relationships between the internal structure of the cold cap, its properties, its thickness, and the internal heat transfer. This contribution shows the distribution of major crystalline phases and the cumulative evolution of gases within the cold cap. It also examines the temperature, conversion degree, and heating rate the melter feed is experiencing during the passage through the cold cap and their effects on the cold-cap bottom temperature and morphology, which are important for the computational fluid dynamics simulations of melters.

36 MATERIALS SCIENCE↗

Atomic Gradient Structure Alters Electronic Structure in 3D across the Bulk and Enhances Photoactivity

Abstract Understanding structure–function relationships enables the design of materials with tailored functionalities. The long‐standing challenge is to design materials with high active volume to improve efficiency. Tailored grain boundaries and lattice defects are traditionally used to tune the electronic structure near interfaces or defects to promote electron and hole separation. However, the active volume of point defect sites or interfaces in these traditional photocatalysts is extremely low. This study reports a structure with continuous atomic positional deformation across the bulk, altering the electronic structure in 3D and creating a significantly higher active volume. Such a structure in anatase is obtained and tuned by phase transformation during the heating process. Transmission electron microscopy and density functional theory results reveal that atomic deformations result in continuous band bending across the particles, facilitating electron–hole separation, inhibiting their recombination, and inducing dramatically enhanced photoactivity. These findings enable a different materials design paradigm that can potentially be harnessed for a broad range of applications.

Ren, Peng↗

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗

Insulator–metal transition in CrSiTe 3 triggered by structural distortion under pressure

van der Waals solids are well known to host remarkable phase diagrams with competing phases, unusual energy transfer processes, and elusive states of matter. Among this class of materials, chalcogenides have emerged as the most flexible and relevant platforms for unraveling charge–structure–function relationships. In order to explore the properties of complex chalcogenides under external stimuli, we measured the far infrared spectroscopic response of CrSiTe 3 under extreme pressure–temperature conditions. Analysis of the 368 cm –1 Si–Te stretching mode and the manner in which it is screened by the closure of the indirect gap reveals that the insulator–metal transition takes place immediately after the structural phase transition—once the mixed phase aspect of the lattice distortion is resolved. At the same time, the two-phase region associated with the structural transition widens with decreasing temperature, and the slope of the insulator–metal transition under pressure is consistent with increasing entropy. These trends completely revise the character of the temperature–pressure phase diagram as well as the relationship between the structural and insulator–metal transitions, leading to a critical nexus of activity that may hide a quantum critical point and allow superconductivity to emerge.

36 MATERIALS SCIENCE↗

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

59 BASIC BIOLOGICAL SCIENCES↗

Structure–performance relationships of lithium-ion battery cathodes revealed by contrast-variation small-angle neutron scattering

Lithium-ion battery cathodes are porous composites of active material, conductive carbon, and polymer binder. Controlling the cathode microstructure is key to achieving high energy density and cycling stability. Current characterization techniques lack the nanoscale resolution over representative volumes necessary to relate cathode microstructure to cycling performance. To address this challenge, we utilize contrast-variation small-angle neutron scattering to quantify the chemical and structural features of cathodes wet by dimethyl carbonate, representing a relevant solvent environment. Using neutron scattering measurements, we identify an expansion in carbon and polymer structures that arises after calendering and wetting with solvent. Further, we deconvolute the carbon and binder phases to obtain the solvent-accessible carbon black surface area, which we correlate to diminished capacity retention driven by electrolyte decomposition on exposed carbon. This technique provides nanoscale insight into composite cathode microstructures and resulting cycling performance, promising future applications to a broad range of porous materials that exist in energy storage systems.

25 ENERGY STORAGE↗