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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Prediction of dynamic behavior of a system undergoing an exchange of components using a transmission simulator method

In systems with modular design, it is of interest to perform component exchanges to upgrade components and explore new system configurations. If the dynamics of the components are known, then dynamic substructuring can be used to obtain a prediction of system performance for the new configuration. The transmission simulator method is a substructuring technique that utilizes an additional fixture to apply an elastic boundary condition to a test article such that an appropriate dynamic response can be obtained for a given substructuring application, and the technique has been used widely for performing coupling and decoupling operations. Here, in this work, a modified transmission simulator method is proposed that allows a direct exchange of components to be performed. In a numerical demonstration, the proposed method is shown to accurately predict the dynamics of an assembly that has undergone a component exchange in which the exchanged components have different material properties and different geometric properties. This approach can be applied to dynamic qualification frameworks in which structures undergo modifications or upgrades rather than complete redesigns.

Component exchange↗
DOE OSTI2021

The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair

Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effect of Ligand Chemistry on the Electronic Properties and Reactivity of Cobalt Acetate Autoxidation Catalysts

Autoxidation chemistry catalyzed by cobalt(II) acetate is an industrial pathway for converting hydrocarbons into oxygenated compounds and has promising potential applications in plastic waste deconstruction. However, the chemical properties of the Co acetate-based catalysts and their roles in the reaction mechanism are poorly understood, and as a result, attempts to redesign the autoxidation chemical process for novel applications lack clear direction. In this work, we investigate the structure and electronic properties of a series of multinuclear Co(III) compounds that have been proposed as active participants in catalytic autoxidation. Through a combination of X-ray spectroscopic measurements [Co K-edge X-ray absorption spectroscopy (XAS), extended X-ray absorption fine structure (EXAFS), Kβ X-ray emission spectroscopy (XES), and high-energy resolution fluorescence detection (HERFD) XAS] and theoretical methods, we characterize the interactions of Co with acetate and hydroxyl ligands in these compounds. Here we show that the substitution of acetate ligands with hydroxyls in these compounds causes an increase in the electron density on Co, driven by the loss of a π back-bonding interaction between Co and acetate and an increase in electron donation to Co from the hydroxyl ligands. We further classify the bonding between Co and acetate based on the orbital overlap and show that the experimental absorption and emission spectra are well-described by the resulting molecular orbitals. Finally, we predict the impacts of acetate/hydroxyl ligand exchange on autoxidation catalytic properties, showing that the reaction free energies for key Co oxidation and reduction steps are extremely sensitive to metal-ligand bonding interactions and thus have meaningful impacts on overall reactivity. The results of this study constitute an important set of design criteria for developing novel homogeneous autoxidation catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Renewable and Biodegradable Polyurethane Foams with Aliphatic Diisocyanates

The transition to renewable plastics will require the development of substitutes with existing industrial standards and manufacturing processes. Polyurethanes (PU), versatile plastics, are traditionally dominated by aromatic diisocyanates, which are challenging to derive from renewable sources. However, for higher biocontent, it is crucial to utilize aliphatic diisocyanates, which can be sourced from renewable plant or algae waste streams. Historically, PU foams relied on aromatic diisocyanates for essential hard segments, resulting in desired physical properties. Here, we report the generation of high-performance renewable and biodegradable PU foams utilizing aliphatic diisocyanates and aromatic polyols, translating hard segments into the polyester polyol component using biosourced furan dicarboxylic acid (FDCA) monomers. We demonstrate that an FDCA-based PU is suitable for foams with performance characteristics that meet commercial tolerances and can biodegrade under backyard compost conditions. Here, this demonstrates steps toward redesigning traditional petrochemical-based polymers to accommodate new biological monomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Optimizing the Solvent Reorganization Free Energy by Metal Substitution for Nanocage Catalysis

The supramolecular capsule Ga 4 L 6 12– has been found to catalyze a number of important chemical reactions, but the close proximity of a poorly organized external solvent environment can serve as an impediment to the reaction chemistry. Here, using ab initio molecular dynamic calculations and electric field analyses, we find that metal substitution of indium for gallium lowers the total and electrostatic activation barriers by ~3–4 kcal/mol in water solvent. Using an energy decomposition analysis of the interaction of water solvent with the metal vertices, we find that Pauli repulsion between the metal and water decreases, allowing the water coordination with the metal to increase, upon substitution of In for Ga. We therefore determine that the stabilization of the transition state is due to a better arrangement of water molecules around the metal vertices of In 4 L 6 12– and provides a proof of concept of how to redesign the nanocage scaffold in order to reduce the solvent reorganization energy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Fractionation of Oxygen Isotopes in Uranium Oxides during Peroxide Precipitation and Dry Air Calcination

The interaction between uranium and oxygen-containing substrates is nearly ubiquitous within the nuclear fuel cycle. Given the well-known and predictable oxygen stable isotope compositions of atmospheric oxygen and meteoric waters around the world, the use of these isotopes as a potential geolocation or processing signature of uranium compounds has been of interest within the nuclear safeguards community. This study focuses on measuring the oxygen-stable isotope composition of synthetically produced uranium oxides to determine the mechanism and extent of fractionation during materials processing relevant to the nuclear fuel cycle. Here, metastudtite [UO 2 O 2 (H 2 O) 2 ] samples were first produced using water and hydrogen peroxide of a known oxygen isotope composition. This starting material was calcined in dry air at temperatures ranging from 300 °C to 1000 °C for 20 h producing oxides ranging in composition from UO 3 +x (0 ≤ x ≤ 0.5) to U 3 O 8 . In addition, calcinations between 500 and 800 °C were performed at different time intervals to evaluate the rate of isotopic equilibration. The δ 18 O values of water bound to metastudtite were measured by thermogravimetric analysis coupled to isotope ratio infrared spectroscopy (TGA–IRIS). A redesigned fluorination manifold was constructed at the University of Utah and was used to extract the bulk oxygen from precipitated and calcined products using bromine pentafluoride (BrF 5 ). Mineralization water on metastudtite (measured by TGA–IRIS) was closely associated with the aqueous environment of precipitation with a fractionation of +3.5 ± 0.6‰. In contrast, bulk oxygen from metastudtite (measured by fluorination and gas chromatography combined with isotope ratio mass spectrometry) was found to have an inconsistent fractionation with precipitation water. Samples calcined in dry air exhibited a wide range of oxygen isotope compositions which increased from δ 18 O = +1.4 ± 0.9‰ at 300 °C to +17.3 ± 0.9‰ at 1000 °C. This variation in δ 18 O values was a result of oxygen exchange with atmospheric O 2 and was found to be rapid at calcination temperatures greater than 600°C—with equilibration occurring in less than 2 h. These results provide insights into the incorporation and exchange of oxygen isotopes during precipitation and calcination processes comparable to those employed within the nuclear fuel cycle and establish a foundation for future investigations to build upon.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Design Criteria of Dilute Ether Electrolytes toward Reversible and Fast Intercalation Chemistry of Graphite Anode in Li-Ion Batteries

To date, dilute ether electrolytes have been believed to be incompatible with graphite in Li-ion batteries due to the detrimental solvent cointercalation and graphite exfoliation. Here, in this paper, we provide design criteria of dilute ether electrolytes for a reversible graphite anode based on tailoring the solvation structures and thermodynamic properties. We clarify that ether solvents can support graphite reversibly by modulating the anion. Our redesigned electrolyte consisting of a single-solvent 1,3-dioxolane (DOL) and 1 M single-salt lithium bis(fluorosulfonyl)imide (LiFSI) shows weakened Li-solvent interaction and results in an inorganic-rich solid-electrolyte interphase. Consequently, we achieved ~99.9% Coulombic efficiency with >96% capacity retention (~350 mAh/g) after 300 cycles at C/5 using natural graphite. The weakly solvated electrolyte maintains desirable transport properties, enabling better rate capability than carbonate electrolytes with an areal capacity of 2–4 mAh/cm 2 . We have demonstrated the potential of dilute ether electrolytes for facile desolvation-based intercalation chemistry in graphite, creating a viable path toward fast-charge Li batteries.

25 ENERGY STORAGE↗
DOE OSTI2022

Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme

We report the past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an “excited-state enzyme”. Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Topology-Accelerated and Selective Cascade Depolymerization of Architecturally Complex Polyesters

Despite considerable recent advances already made in developing chemically circular polymers (CPs), the current framework predominantly focuses on CPs with linear-chain structures of different monomer types. As polymer properties are determined by not only composition but also topology, manipulating the topology of the single-monomer-based CP systems from linear-chain structures to architecturally complex polymers could potentially modulate the resulting polymer properties without changing the chemical composition, thereby advancing the concept of monomaterial product design. To that end, here, we introduce a chemically circular hyperbranched polyester (HBPE), synthesized by a mixed chain-growth and step-growth polymerization of a rationally designed bicyclic lactone with a pendent hydroxyl group (BiLOH). This HBPE exhibits full chemical recyclability despite its architectural complexity, showing quantitative selectivity for regeneration of BiLOH, via a unique cascade depolymerization mechanism. Moreover, distinct differences in materials properties and performance arising from topological variations between HBPE, hb-PBiLOH, and its linear analogue, l-PBiLOH, have been revealed where generally the branched structure led to more favorable interchain interactions, and topology-amplified optical activity has also been observed for chiral (1S, 4S, 5S)-hb-PBiLOH. More intriguingly, depolymerization of l-PBiLOH proceeds through an unexpected, initial topological transformation to the HBPE polymer, followed by the faster cascade depolymerization pathway adopted by hb-PBiLOH. Overall, these results demonstrate that CP design can go beyond typical linear polymers, and rationally redesigned, architecturally complex polymers for their unique properties may synergistically impart advantages in topology-augmented depolymerization acceleration and selectivity for exclusive monomer regeneration.

depolymerization↗
DOE OSTI2023

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Inter-cofactor protein remodeling rewires short-circuited transmembrane electron transfer

Intraprotein electron transfer (ET) requires explicit local control of the environment of cofactors to influence their intermolecular distances, relative orientations, and redox properties. Efficient, longer-range ET often utilizes molecular orbitals of aromatic residues present in the intervening space. Here, revitalization of a vestigial ET pathway in the bacterial photosynthetic reaction center is achieved by scanning with tryptophans to uncover markedly improved routes of electron conduction in a key stabilizing step spanning 15 Å between tetrapyrrole and quinone cofactors. This ET event is maximally enhanced by pairing one or more tryptophans with a threonine to influence quinone binding and/or redox potential. Synergistic effects of these substitutions increase the yield of that ET step to ~95%. Joining these substitutions with mutant residues that improve initial ET steps dramatically enhances transmembrane charge separation via this redesigned version of a pathway that is quantitatively inactive in the native protein-cofactor complex.

Biophysical chemistry↗
DOE OSTI2020

Flexible metal–gas batteries: a potential option for next-generation power accessories for wearable electronics

Flexible metal–gas batteries have become increasingly attractive for use in wearable electronics in the recent years due to their large theoretical energy density and superior adaptability to irregular geometric surfaces, such as the human body. With continuous improvements in design strategies and assembly technologies, the fabrication of various advanced flexible metal–gas batteries has been attempted. In spite of these efforts, the synchronous integration of high flexibility, safety, comfort, and high performance into flexible metal–gas batteries with specifically functionalized configurations still remains a formidable challenge. To resolve these dilemmas, the redesign of cathode catalysts, gel polymer electrolyte, and battery configurations/components has been investigated. In this paper, we review the recent technical advances together with the major dilemmas facing currently available flexible metal–gas batteries, highlighting how flexible cathodes and gel polymer electrolytes with various structures and components can affect the electrochemical performance and functionality of flexible metal–gas batteries. Flexible Zn–air, Li–O 2 /air, and Li–CO 2 batteries are mainly exemplified to elucidate their promising potential. Finally, based on our considerations, unresolved technical hurdles and future research perspectives involving flexible metal–gas batteries for wearable electronics are proposed.

25 ENERGY STORAGE↗
DOE OSTI2025

Enhancing generative molecular design via uncertainty-guided fine-tuning of variational autoencoders

In recent years, deep generative models have been successfully applied to various molecular design tasks, particularly in the life and materials sciences. One critical challenge for pre-trained generative molecular design (GMD) models is to fine-tune them to be better suited for downstream design tasks that aim at optimizing specific molecular properties. However, redesigning and training an existing effective generative model from scratch for each new design task are impractical. Furthermore, the black-box nature of typical downstream tasks that involve property prediction makes it nontrivial to optimize the generative model in a task-specific manner. In this work, we propose an uncertainty-guided fine-tuning strategy that can effectively enhance a pre-trained variational autoencoder (VAE) for GMD through performance feedback in an active learning setting. The strategy begins by quantifying the model uncertainty of the generative model using an efficient active subspace-based UQ (uncertainty quantification) scheme. Next, the decoder diversity within the characterized model uncertainty class is explored to expand the viable space of molecular generation. The low-dimensionality of the active subspace makes this exploration tractable using a black-box optimization scheme, which in turn enables us to identify and leverage a diverse set of high-performing models to generate enhanced molecules. Empirical results across six target molecular properties using multiple VAE-based generative models demonstrate that our uncertainty-guided fine-tuning strategy consistently leads to improved models that outperform the original pre-trained models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Development of a Versatile, Full-featured Search Functionality for Indico

Indico, CERN’s popular open-source tool for event management, is in widespread use among facilities that make up the HEP community. It is extensible through a robust plugin architecture that provides features such as search and video conferencing integration. In 2018, Indico version 2 was released with many notable improvements, but without a full-featured search functionality that could be implemented easily outside of CERN. At both Fermi and Brookhaven National Laboratories, the user community viewed the lack of this popular feature as a significant impediment to deployment of the new software. In the meantime, CERN embarked upon a major redesign of their core search service, one that would also necessitate a rewrite of the Indico search interface. Seeing this pressing need, the two US labs decided to collaborate, with assistance from the CERN development team, on a project to develop the requisite search functionality for the larger user community. The resulting design exploits the simplified schema defined in the new CERN Search micro-service, based on Invenio and Elasticsearch, while still providing a flexible path to implementation for alternative backend search services. It is intended to provide a software package that can be installed easily and used out of the box, by anyone at any site. This paper will discuss the design choices and architectural challenges, and provide an overview of the deployment and use of these new plugins.

Constanta, Penelope↗
DOE OSTI2024

Multithreading ATLAS offline software: A retrospective

For Run 3, ATLAS redesigned its offline software, Athena, so that the main workflows run completely multithreaded. The resulting substantial reduction in the overall memory requirements allows for better use of machines with many cores. This note will discuss the performance achieved by the multithreaded reconstruction, the process of migrating the large ATLAS code base, and tools and techniques that were useful in debugging threading-related problems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗