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At least 289 records · Page 16

The Rise of Neural Networks for Materials and Chemical Dynamics

Machine learning (ML) is quickly becoming a premier tool for modeling chemical processes and materials. ML-based force fields, trained on large data sets of high-quality electron structure calculations, are particularly attractive due their unique combination of computational efficiency and physical accuracy. This Perspective summarizes some recent advances in the development of neural network-based interatomic potentials. Designing high-quality training data sets is crucial to overall model accuracy. One strategy is active learning, in which new data are automatically collected for atomic configurations that produce large ML uncertainties. Another strategy is to use the highest levels of quantum theory possible. Transfer learning allows training to a data set of mixed fidelity. A model initially trained to a large data set of density functional theory calculations can be significantly improved by retraining to a relatively small data set of expensive coupled cluster theory calculations. These advances are exemplified by applications to molecules and materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring nuclear structure with multiparticle azimuthal correlations at the LHC

Details of the nuclear structure of Xe, such as the quadrupole deformation and the nuclear diffuseness, are studied by extensive measurements of anisotropic-flow-related observables in Xe–Xe collisions at a centre-of-mass energy per nucleon pair $\sqrt{s_{NN}}$ = 5.44 TeV with the ALICE detector at the LHC. The results are compared with those from Pb–Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV for a baseline, given that the 208 Pb nucleus exhibits a very weak deformation. Furthermore, comprehensive comparisons are performed with a state-of-the-art hybrid model using IP-Glasma+MUSIC+UrQMD. It is found that among various IP-Glasma+MUSIC+UrQMD calculations with different values of nuclear parameters, the one using a nuclear diffuseness parameter of α 0 = 0.492 and a nuclear quadrupole deformation parameter of β 2 = 0.207 provides a better description of the presented flow measurements. These studies represent the first systematic exploration of nuclear structure at TeV energies, utilizing a comprehensive set of anisotropic flow observables. The measurements serve as a critical experimental benchmark for rigorously testing the interplay between nuclear structure inputs and heavy-ion theoretical models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Structure and Filler on Mechanical Properties of Direct Ink Write Pads

Direct ink write (DIW) is an extrusion-based additive manufacturing (AM) technique that enables superior repeatability, property tuning, and material customization compared to conventional manufacturing techniques. In this research, DIW is used to print silicone foams that must accommodate the thermal expansion of other parts. This expansion requires the material to compress and subsequently recover. Thus, a key performance metric is reducing “compression set” or deformation retained after the material is compressed. For this study, a silicone resin was compounded with a getter material, 1,4 bis(phenylethynyl)benzene (DEB) mixed with carbon-supported palladium (Pd) and printed in a variety of lattice structures. The effects of the filler and print structure on compression set were evaluated. In these experiments, 0.5-inch diameter coupons were compressed to 75% their original height for 22 hours at 70 °C, and the change in height calculated at intervals between 30 minutes and 24 hours post-decompression. The unfilled pad with skin layers had the best compression set at 0.7% ± 0.1%, followed by the unfilled pad with no skins at 1.5% ± 0.1%. As the number of filled layers increased, compression set performance degraded. The pad with filled skin layers and all filled layers had a compression set of 7.0% ± 0.3%. Additionally, the reaction extent of DEB was found to increase compression set, possibly due to the diffusion of DEB to the surface at elevated temperatures. Imaging reveals extensive crystallization at the surface. These investigations show that a non-reinforcing filler will increase compression set but that print structure can mitigate this effect.

36 MATERIALS SCIENCE↗

Development of molecular cluster models to probe pyrite surface reactivity

Abstract The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic‐scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n (FeS 2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe (II) sites that are connected via a range of persulfide (S 2 2− ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS 2 units, we established guidelines for obtaining low‐energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano‐reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron‐transfer reactions can occur.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Moving closer to experimental level materials property prediction using AI

Abstract While experiments and DFT-computations have been the primary means for understanding the chemical and physical properties of crystalline materials, experiments are expensive and DFT-computations are time-consuming and have significant discrepancies against experiments. Currently, predictive modeling based on DFT-computations have provided a rapid screening method for materials candidates for further DFT-computations and experiments; however, such models inherit the large discrepancies from the DFT-based training data. Here, we demonstrate how AI can be leveraged together with DFT to compute materials properties more accurately than DFT itself by focusing on the critical materials science task of predicting “formation energy of a material given its structure and composition”. On an experimental hold-out test set containing 137 entries, AI can predict formation energy from materials structure and composition with a mean absolute error (MAE) of 0.064 eV/atom; comparing this against DFT-computations, we find that AI can significantly outperform DFT computations for the same task (discrepancies of $$>0.076$$ > 0.076 eV/atom) for the first time.

36 MATERIALS SCIENCE↗

Uncertainty Quantification in CO2 Trapping Mechanisms: A Case Study of PUNQ-S3 Reservoir Model Using Representative Geological Realizations and Unsupervised Machine Learning

Evaluating uncertainty in CO2 injection projections often requires numerous high-resolution geological realizations (GRs) which, although effective, are computationally demanding. This study proposes the use of representative geological realizations (RGRs) as an efficient approach to capture the uncertainty range of the full set while reducing computational costs. A predetermined number of RGRs is selected using an integrated unsupervised machine learning (UML) framework, which includes Euclidean distance measurement, multidimensional scaling (MDS), and a deterministic K-means (DK-means) clustering algorithm. In the context of the intricate 3D aquifer CO2 storage model, PUNQ-S3, these algorithms are utilized. The UML methodology selects five RGRs from a pool of 25 possibilities (20% of the total), taking into account the reservoir quality index (RQI) as a static parameter of the reservoir. To determine the credibility of these RGRs, their simulation results are scrutinized through the application of the Kolmogorov–Smirnov (KS) test, which analyzes the distribution of the output. In this assessment, 40 CO2 injection wells cover the entire reservoir alongside the full set. The end-point simulation results indicate that the CO2 structural, residual, and solubility trapping within the RGRs and full set follow the same distribution. Simulating five RGRs alongside the full set of 25 GRs over 200 years, involving 10 years of CO2 injection, reveals consistently similar trapping distribution patterns, with an average value of Dmax of 0.21 remaining lower than Dcritical (0.66). Using this methodology, computational expenses related to scenario testing and development planning for CO2 storage reservoirs in the presence of geological uncertainties can be substantially reduced.

Mahjour, Seyed Kourosh↗

Biopolymer Concrete

Cement production for concrete has been responsible for ~7–8% of global greenhouse gas (GHG) emissions, and nearly equally contribution for steel production processes (EPA, 2020). In order to achieve carbon neutrality by 2050, a novel solution has to be investigated. This project aims to develop fundamental mechanistic understanding and experimental characterization to create a 3D printable biopolymer concrete using plant-based polyurethane as an innovative and sustainable alternative for Portland cement concrete, with significantly low carbon footprint. Future construction will utilize the advances in digital additive manufacturing (3D printing) to produce optimal geometries with a minimum waste of materials. Understanding the polymerization process, factors impacting the composite rheology, and the structural behavior of this biopolymer concrete will enable us to engineer the next generation of concrete structures with low carbon footprint. This project aims to improve the nation’s ability to control Greenhouse Gas emission neutrality for the set goal of 2050 via introducing a structurally viable bio-based polymer concrete.

42 ENGINEERING↗

Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments

Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C 4 H 4 N may contribute to this signature. We have characterized seven isomers of C 4 H 4 N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH 2 CCHCNH + , a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C 4 H 4 N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction

The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-reaching implications for a range of problems, including metabolomics. However, problems such as predicting the bound structure of a protein–ligand complex along with its affinity have proven to be an enormous challenge. In recent years, machine learning-based methods have proven to be more accurate than older methods, many based on simple linear regression. Nonetheless, there remains room for improvement, as these methods are often trained on a small set of features, with a single functional form for any given physical effect, and often with little mention of the rationale behind choosing one functional form over another. Moreover, it is not entirely clear why one machine learning method is favored over another. Here, we endeavor to undertake a comprehensive effort towards developing high-accuracy, machine-learned scoring functions, systematically investigating the effects of machine learning method and choice of features, and, when possible, providing insights into the relevant physics using methods that assess feature importance. Here, we show synergism among disparate features, yielding adjusted R 2 with experimental binding affinities of up to 0.871 on an independent test set and enrichment for native bound structures of up to 0.913. When purely physical terms that model enthalpic and entropic effects are used in the training, we use feature importance assessments to probe the relevant physics and hopefully guide future investigators working on this and other computational chemistry problems.

59 BASIC BIOLOGICAL SCIENCES↗

Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes

Insects known as leafhoppers (Hemiptera: Cicadellidae) produce hierarchically structured nanoparticles known as brochosomes that are exuded and applied to the insect cuticle, thereby providing camouflage and anti-wetting properties to aid insect survival. Although the physical properties of brochosomes are thought to depend on the leafhopper species, the structure–function relationships governing brochosome behavior are not fully understood. Brochosomes have complex hierarchical structures and morphological heterogeneity across species, due to which a multimodal characterization approach is required to effectively elucidate their nanoscale structure and properties. In this work, we study the structural and mechanical properties of brochosomes using a combination of atomic force microscopy (AFM), electron microscopy (EM), electron tomography, and machine learning (ML)-based quantification of large and complex scanning electron microscopy (SEM) image data sets. This suite of techniques allows for the characterization of internal and external brochosome structures, and ML-based image analysis methods of large data sets reveal correlations in the structure across several leafhopper species. Our results show that brochosomes are relatively rigid hollow spheres with characteristic dimensions and morphologies that depend on leafhopper species. Nanomechanical mapping AFM is used to determine a characteristic compression modulus for brochosomes on the order of 1–3 GPa, which is consistent with crystalline proteins. Altogether, this work provides an improved understanding of the structural and mechanical properties of leafhopper brochosomes using a new set of ML-based image classification tools that can be broadly applied to nanostructured biological materials.

Chemical structure↗

NSO Processing Scripts (NSO wind loading data set processing scripts) [SWR-23-86]

NREL conducted comprehensive field measurements of the atmospheric turbulent wind conditions and the resulting structural wind loads on parabolic troughs at the Nevada Solar One plant from October 2021 to June, 2023. The measurement set-up included meteorological masts and structural load sensors on four trough rows. Additionally, NREL commissioned a lidar scanning the horizontal plane over the trough field. The high-resolution data set, characterizing the complex flow field and resulting structural loads, is available at https://data.openei.org/submissions/5938. The processing routines published here were used to create the data from the instruments' raw data.

Egerer, Ulrike↗

Bill Savings vs. Backup Power: Evaluating operational tradeoffs for home solar+storage systems [Slides]

This study explores tradeoffs between the use of home solar+storage systems for backup power versus day-to-day utility bill savings. The study focuses specifically on the “reserve setting” available with most home battery storage systems, which allow the customer to maintain some minimum level of storage in reserve in case of an unforeseen power interruption. The more capacity that is held in reserve, the greater the customer’s ability to ride-through possible power interruptions, but less capacity is then available to manage utility bills on a day-to-day basis. This study evaluates this operational tradeoff across a diverse set of locations and residential electricity tariff structures, relying on Berkeley Lab’s PRESTO model to stochastically simulate power interruption events, and exploring a range of sensitivities, including variations in customer value of lost load (VoLL), interruption frequency, and other key drivers. The results show that, in most circumstances, the opportunity cost of holding storage capacity in reserve, in terms of foregone bill saving, tends to outweigh any gains in reliability value associated with mitigated power interruptions. This finding is robust across tariff structures and across most of the sensitivities considered, including those related to rate level, customer load level, and storage sizing. There are a limited set of circumstances where raising the reserve setting improves the overall customer value (comprised of bill savings plus reliability value). Specifically, that exception occurs when all of the following conditions apply: (a) the customer resides in a location with exceptionally poor reliability, (b) the customer has exceptionally high VoLL; (c) the customer is on a net billing rate or on a TOU rate that allows grid discharging but not grid charging; and (d), depending on the location, the price arbitrage differential on that rate is relatively small. In all other circumstances analyzed, total customer value declines with reserve level.

14 SOLAR ENERGY↗

Multi-Level Structural Damage Characterization Using Sparse Acoustic Sensor Networks and Knowledge Transferred Deep Learning

Standard structural health monitoring techniques face well-known difficulties for comprehensive defect diagnosis in real-world structures that have structural, material, or geometric complexity. This motivates the exploration of machine-learning-based structural health monitoring methods in complex structures. However, creating sufficient training data sets with various defects is an ongoing challenge for data-driven machine (deep) learning algorithms. The ability to transfer the knowledge of a trained neural network from one component to another or to other sections of the same component would drastically reduce the required training data set. Also, it would facilitate computationally inexpensive machine learning based inspection systems. In this work, a machine-learning-based multi-level damage characterization is demonstrated with the ability to transfer trained knowledge within the sparse sensor network. A novel network spatial assistance and an adaptive convolution technique are proposed for efficient knowledge transfer within the deep learning algorithm. Proposed structural health monitoring method is experimentally evaluated on an aluminum plate with artificially induced defects. It was observed that the method improves the performance of knowledge transferred damage characterization by 50% during localization and 24% during severity assessment. Further, experiments using time windows with and without multiple edge reflections are studied. Results reveal that multiply scattered waves contain rich and deterministic defect signatures that can be mined using deep learning neural networks, improving the accuracy of both identification and quantification. In the case of a fixed sensor network, using multiply scattered waves shows 100% prediction accuracy at all levels of damage characterization.

36 MATERIALS SCIENCE↗

Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe 4S] Fd activity

Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1 T11I ). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1 T11I . Electrochemical characterization revealed both Fer1 and Fer1 T11I have similar redox transitions (–480 mV and – 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron-sulfur (Fe—S) cluster of Fer1. Additionally, disruption of hydrogen bonding around an Fe—S cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1 T11I . Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1 T11I , which indicate changes to the high spin states and/or spin-spin coupling between the Fe—S clusters of Fer1. Finally, our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗

High-power test of a C-band linear accelerating structure with an RFSoC-based LLRF system

Normal conducting linear particle accelerators consist of multiple rf stations with accelerating structure cavities. Low-level rf (LLRF) systems are employed to set the phase and amplitude of the field in the accelerating structure and to compensate for the pulse-to-pulse fluctuation of the rf field in the accelerating structures with a feedback loop. The LLRF systems are typically implemented with analog rf mixers, heterodyne-based architectures, and discrete data converters. There are multiple rf signals from each of the rf stations, so the number of rf channels required increases rapidly with multiple rf stations. With a large number of rf channels, the footprint, component cost, and system complexity of the LLRF hardware will increase significantly. To meet the design goals of being compact and affordable for future accelerators, we have designed the next-generation LLRF (NG-LLRF) with a higher integration level based on RFSoC technology. The NG-LLRF system samples rf signals directly and performs rf mixing digitally. Further, the NG-LLRF has been characterized in loopback mode to evaluate the performance of the system and has also been tested with a standing-wave accelerating structure, a prototype for the Cool Copper Collider (C 3 ) with a peak rf power level up to 16.45 MW. The loopback test demonstrated amplitude fluctuation below 0.15% and phase fluctuation below 0.15°, which are considerably better than the requirements of C 3 . The rf signals from the different stages of the accelerating structure at different power levels are measured by the NG-LLRF, which will be critical references for the control algorithm designs. The NG-LLRF also offers flexibility in waveform modulation, so we have used rf pulses with various modulation schemes, which could be useful for controlling some of the rf stations in accelerators. In this paper, the high-power test results at different stages of the test setup will be summarized, analyzed, and discussed.

47 OTHER INSTRUMENTATION↗

Building Structure-Property Relationships of Cycloalkanes in Support of Their Use in Sustainable Aviation Fuels

In 2018 13.7 EJ of fuel were consumed by the global commercial aviation industry. Worldwide, demand will increase into the foreseeable future. Developing Sustainable Aviation Fuels (SAFs), with decreased CO 2 and soot emissions, will be pivotal to the on-going mitigation efforts against global warming. Minimizing aromatics in aviation fuel is desirable because of the high propensity of aromatics to produce soot during combustion. Because aromatics cause o-rings to swell, they are important for maintaining engine seals, and must be present in at least 8 vol% under ASTM-D7566. Recently, cycloalkanes have been shown to exhibit some o-ring swelling behavior, possibly making them an attractive substitute to decrease the aromatic content of aviation fuel. Cycloalkanes must meet specifications for a number of other physical properties to be compatible with jet fuel, and these properties can vary greatly with the cycloalkane chemical structure, making their selection difficult. Building a database of structure-property relationships (SPR) for cycloalkanes greatly facilitates their furthered inclusion into aviation fuels. The work presented in this paper develops SPRs by building a data set that includes physical properties important to the aviation industry. The physical properties considered are energy density, specific energy, melting point, density, flashpoint, the Hansen solubility parameter, and the yield sooting index (YSI). Further, our data set includes cycloalkanes drawn from the following structural groups: fused cycloalkanes, n-alkylcycloalkanes, branched cycloalkanes, multiple substituted cycloalkanes, and cycloalkanes with different ring sizes. In addition, a select number of cycloalkanes are blended into Jet-A fuel (POSF-10325) at 10 and 30 wt%. Comparison of neat and blended physical properties are presented. One major finding is that ring expanded systems, those with more than six carbons, have excellent potential for inclusion in SAFs. Our data also indicate that polysubstituted cycloalkanes have higher YSI values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗