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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural Insights into Mechanisms Underlying Mitochondrial and Bacterial Cytochrome c Synthases

Mitochondrial holocytochrome c synthase (HCCS) is an essential protein in assembling cytochrome c (cyt c) of the electron transport system. HCCS binds heme and covalently attaches the two vinyls of heme to two cysteine thiols of the cyt c CXXCH motif. Human HCCS recognizes both cyt c and cytochrome c1 of complex III (cytochrome bc1). HCCS is mutated in some human diseases and it has been investigated recombinantly by mutational, biochemical, and reconstitution studies in the past decade. Here, we employ structural prediction programs (e.g., AlphaFold 3) on HCCS and its two substrates, heme and cytochrome c. The results, when combined with spectroscopic and functional analyses of HCCS and variants, provide insights into the structural basis for heme binding, apocyt c binding, covalent attachment, and release of the holocyt c product. Results from in vitro reconstitution of purified human HCCS using cyt c and cyt c1 peptides as acceptors are consistent with the structural modeling of substrate binding. Reconstitution of HCCS and cyt c1 provides an approach to studying cyt c1 assembly, which has been refractile to recombinant in vivo reconstitution (unlike HCCS and cyt c). We propose a structural basis for release of the holocyt c product from HCCS based on in vitro studies and on cryoEM structures of the bacterial cyt c synthase (CcsBA) active site. We analyze the kinetoplastid mitochondrial synthase (KCCS), and hypothesize a molecular evolutionary path from mitochondrial endosymbiosis to the current HCCS.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Optimized Auxiliary Functions for Robust Mitigation of Finite-Size Errors in Periodic Hybrid Density Functional Theory

When calculating properties of periodic systems at the thermodynamic limit (TDL), the dominant source of finite size error (FSE) arises from the long-range Coulomb interaction, and can manifest as a slowly converging quadrature error when approximating an integral in the reciprocal space by a finite sum. The singularity subtraction (SS) method offers a systematic approach for reducing this quadrature error and thus the FSE. Here, in this work, we first investigate the performance of the SS method in the simplest setting, aiming at reducing the FSE in exact exchange calculations by subtracting the Coulomb contribution with a single, adjustable Gaussian auxiliary function. We demonstrate that a simple fitting method can robustly estimate the optimal Gaussian width and leads to rapid convergence toward the TDL. Furthermore, we suggest new forms of the auxiliary function, whose optimal parameters could also be determined through least-squares fitting. For a range of semiconductors and insulators, the proposed auxiliary functions achieve robust, millihartree-level accuracy in hybrid density functional theory calculations, including cases with sparse k-meshes and large basis sets.

Quiton, Stephen Jon [University of California, Ber↗
DOE OSTI2024

Putting error bars on density functional theory dataset

This dataset contains submission files and raw output files from high-throughput DFT simulations to analyze the systemic errors in lattice constant, bulk moduli and formation energy predictions for a range of binary and ternary oxides using four exchange correlation functionals (LDA, PBE, PBEsol and vdW-DF-C09). This data was then used as the basis for employing materials informatics methods to predict the expected errors in the lattice constants of the studied compounds. Predicted errors were also used to better the DFT-predicted lattice parameters. Our results emphasize the link between the computed errors and the electron density and hybridization errors of a functional. In essence, these results provide “error bars” for choosing a functional for the creation of high-accuracy, high-throughput datasets as well as avenues for the development of XC functionals with enhanced performance, thereby enabling the accelerated discovery and design of new materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Classical Preoptimization Approach for ADAPT-VQE: Maximizing the Potential of High-Performance Computing Resources to Improve Quantum Simulation of Chemical Applications

The ADAPT-VQE algorithm is a promising method for generating a compact ansatz based on derivatives of the underlying cost function, and it yields accurate predictions of electronic energies for molecules. In this work, we report the implementation and performance of ADAPT-VQE with our recently developed sparse wave function circuit solver (SWCS) in terms of accuracy and efficiency for molecular systems with up to 52 spin orbitals. The SWCS can be tuned to balance computational cost and accuracy, which extends the application of ADAPT-VQE for molecular electronic structure calculations to larger basis sets and a larger number of qubits. Using this tunable feature of the SWCS, we propose an alternative optimization procedure for ADAPT-VQE to reduce the computational cost of the optimization. Furthermore, by preoptimizing a quantum simulation with a parametrized ansatz generated with ADAPT-VQE/SWCS, we aim to utilize the power of classical high-performance computing in order to minimize the work required on noisy intermediate-scale quantum hardware, which offers a promising path toward demonstrating quantum advantage for chemical applications.

ADAPT-VQE↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2024

The atomic-level structure and stability of interfaces of Pt nanoparticles in alumina: An experimental and computational evaluation

The atomic-level structure of interfaces between Pt and a transition form of Al2O3 were studied using a combination of electron microscopy and first principles calculations. A model system of Pt nanoprecipitates in Al2O3 were formed in sapphire wafers via high-energy ion implantation of Pt followed by thermal annealing at 1000 °C in air. The Pt nanoparticles took the form of tetrahedra and truncated tetrahedra primarily bound by {111}Pt facets. The high prevalence of these facets motivated the development of density functional theory (DFT) based models of (111)Pt interfaces with six different chemical terminations of ( 2 ¯ 01 ) θ-alumina. The atomic-level structure of the Pt/Al2O3 interfaces was characterized with aberration-corrected scanning transmission electron microscopy (STEM) and the experimental images were compared to STEM image simulations of the DFT models. The model interface with Pt bonded to oxygen-terminated θ-Al2O3, with the Pt located on top of the O and with an underlying layer of octahedral Al, provided the best match to the experimental images. This interfacial termination is also the most stable for the thermal annealing conditions used based on thermodynamic calculations of the interfacial energy as a function of temperature and oxygen partial pressure. This experimentally verified model provides a basis for improving models of Pt/γ-alumina interfaces.

Clauser, A L↗
DOE OSTI2025

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase

Abstract The average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3′-CCA end in the active site cannot proceed until the lysyl–adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS–tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium toward the 3′-CCA end “docked” conformation and allosterically increases h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.

Devarkar, Swapnil C. (ORCID:000000029271243X)↗
DOE OSTI2026

Universal progression of structure and dynamics in colloidal nanocrystal gels during salt-accelerated aging

Controlling the structure and function of colloidal gels requires a detailed understanding of how the various components govern network formation and aging. In particular, molecular additives like salts are widely used to tune interparticle interactions, yet their influence on gelation pathways in complex systems such as colloidal nanocrystal gels remains inadequately understood. Here, we investigate how noncoordinating salts modulate the evolution of gels formed using chemically linked tin-doped indium oxide nanocrystals. Through combined structural, dynamic, and kinetic analyses, we demonstrate that increasing salt concentration accelerates gelation. When rescaled by salt-dependent characteristic times, the evolution collapses onto universal trajectories, revealing a time-salt superposition principle. The universality extends across length scales, suggesting a consistent salt-dependent mechanism that controls both local structuring and macroscopic network formation. This observed salt modulation of structure and dynamics provides a predictive basis for controlling the kinetics of nonequilibrium nanocrystal gel assembly, enhancing the rational design of functional nanomaterials with tunable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Theoretical and kinetic modeling study of hydrazine oxidation

The present work constitutes the first theoretical and kinetic modeling study of hydrazine oxidation, which may be important for burnout in ammonia-fueled combustion. The kinetics of the oxidation of N 2 H 4 , N 2 H 3 and tHNNH by molecular oxygen were investigated via a quantum chemistry/canonical transition state theory approach. Geometries and anharmonic frequencies were obtained with density functional theory, and energies from coupled cluster calculations (CCSD(T)) extrapolated to the infinite basis set limit, with corrections for core-valence electron correlation, scalar relativistic effects, and higher level correlation up to lambda coupled cluster, CCSDT(Q) Λ . The key reactions occurred on the N 2 H 4 O 2 potential energy surface, where the results indicated a fast reaction of N 2 H 3 with HO 2 via singlet adducts to yield tHNNH + H 2 O 2 and HNN(H)O + H 2 O, while reaction on the triplet surface proceeds via a bound complex followed by a tight, submerged barrier to yield N 2 H 4 + O 2 . The results were incorporated in a detailed reaction mechanism, which was used to interpret the shock tube results from Michel and Wagner (1965) on the effect of O 2 on hydrazine conversion at 1100–1400 K. The kinetic model captured qualitatively the observed behavior, but underestimated the reaction rate under oxidizing conditions. The hydrazine pyrolysis chemistry dominated conversion at reducing conditions and/or high temperature. At oxidizing conditions and intermediate temperatures (≲ 1400 K), reactions of N 2 -amines with HO 2 and O 2 were important for the oxidation rate.

Ab initio calculations↗
DOE OSTI2024

HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics

Abstract During mitosis, microtubule dynamics are regulated to ensure proper alignment and segregation of chromosomes. The dynamics of kinetochore-attached microtubules are regulated by hepatoma-upregulated protein (HURP) and the mitotic kinesin-8 Kif18A, but the underlying mechanism remains elusive. Using single-molecule imaging in vitro, we demonstrate that Kif18A motility is regulated by HURP. While sparse decoration of HURP activates the motor, higher concentrations hinder processive motility. To shed light on this behavior, we determine the binding mode of HURP to microtubules using cryo-EM. The structure helps rationalize why HURP functions as a microtubule stabilizer. Additionally, HURP partially overlaps with the microtubule-binding site of the Kif18A motor domain, indicating that excess HURP inhibits Kif18A motility by steric exclusion. We also observe that HURP and Kif18A function together to suppress dynamics of the microtubule plus-end, providing a mechanistic basis for how they collectively serve in microtubule length control.

Science & Technology - Other Topics↗
DOE OSTI2024

Gravitational form factors of charmonia

We investigate the gravitational form factors of charmonium. Our method is based on a Hamiltonian formalism on the light front known as basis light-front quantization. The charmonium mass spectrum and light-front wave functions were obtained from diagonalizing an effective Hamiltonian that incorporates confinement from holographic QCD and one-gluon exchange interaction from light-front QCD. We proposed a quantum many-body approach to construct the hadronic matrix elements of the energy momentum tensor T + + and T + − , which are used to extract the gravitational form factors A ( Q 2 ) and D ( Q 2 ) . The obtained form factors satisfy the known constraints, e.g., the von Laue condition. From these quantities, we also extract the energy, pressure and light-front energy distributions of the system. We find that hadrons are multilayer systems. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Community Input on the Need, Scope, and Development Roadmap of a Proposed National Virtual Biosecurity for Bioenergy Crops Center (NVBBCC)

Brookhaven National Laboratory (BNL) was awarded a pilot project in FY22 under the U.S. Department of Energy (DOE) Office of Science Biopreparedness Research Virtual Environment (BRaVE) initiative, to define research priorities, needs, and requirements for a national virtual center devoted to the biosecurity of bioenergy crops. The mission of the proposed center, referred to as the National Virtual Biosecurity for Bioenergy Crop Center (NVBBCC), would be to provide the scientific basis and tools to detect, characterize, model, and mitigate biothreats to bioenergy crops. This function will be essential to ensure the projected increased US reliance over the next few decades on key plant-based energy products, such as biojet fuel. The NVBBCC is envisioned as a distributed, virtual center with multiple national laboratories at its core to maximize the use of existing unique facilities and expertise across the DOE complex. A major goal of the pilot project was to develop a roadmap for establishing NVBBCC through a series of meetings to gather community input. A total of about 150 individuals, drawn from DOE laboratories, the USDA, academia, NIH, DHS and the private sector participated in six planning meetings held in FY23. Four of the meetings were focused on specific research topics (disease detection, dispersion and disease propagation, biomolecular characterization of plant-pathogen interaction, and mitigation strategies). These four meetings were followed by a meeting that focused on computational needs to support collaborative, data-intensive research within a distributed center as well as workforce development. A final meeting focused on establishing and maintaining preparedness within NVBBCC to respond to an emerging disease within bioenergy crops and how it would collaborate and coordinate with USDA and DHS.

09 BIOMASS FUELS↗
DOE OSTI2026

Hybrid Cooling and Water Treatment for Resilient, Water-Self-Sufficient Data Centers

The continued growth of data center infrastructure is intensifying demand for freshwater resources, particularly in water-stressed regions, and is increasingly limiting sustainable capacity expansion. This work investigates a conceptual hybrid system that integrates freeze desalination with ultrasonic-assisted ice separation to enable on-site production of pure water from diverse sources, including seawater, brackish groundwater, and reclaimed industrial or agricultural wastewater. Simultaneously, the system produces low-temperature cooling streams that enhance heat removal in high power density computing environments. A process-level thermodynamic analysis is performed across a range of boundary and operating conditions, including variations in feed concentration, freezing temperature, and mass flow rate. The results are presented as performance curves relating feedwater concentration and target purified water output to the corresponding intake flow requirements, enabling estimation of source water demand per unit of Information Technology Equipment (ITE) energy consumption (kWh) across varying data center scales and operational scenarios. The corresponding electrical energy consumption for integrated cooling and water treatment is also evaluated as a function of system operating parameters and target water production levels. These results provide a basis for evaluating system feasibility across different conditions and for identifying parameter ranges in which integrated water treatment and cooling improve resource efficiency, thermal performance, and operational flexibility in data centers.

Elhefny, Aly [ORNL] (ORCID:0000000284907923)↗
DOE OSTI2025

Visualization of Noisy and Less Noisy Computational Basis States in Quantum Computing

Quantum computing technology holds substantial promise as a reliable computational paradigm. However, current noisy intermediate scale quantum (NISQ) systems, are significantly impacted by noise originating from hardware inconsistencies. This noise causes errors and lowers output fidelity. So we must find which basis states cause errors. However, there are two main challenges in analyzing noise corresponding to basis states. First, the noise distribution data is high dimensional in nature, thereby making its analysis challenging. Second, although functional box plots have been used in the state of the art research to understand such a high dimensional data, they suffer from clutter and occlusion issues because of overplotting. In this study, we introduce an innovative visualization pipeline to address the aforementioned challenges to provide a clear depiction of noisy and less-noisy basis states. Specifically, our proposed visualization pipeline comprises three stages namely, low dimensional embedding, clustering, and violin plot visualization, to reduce visual clutter and effectively analyze high-dimensional noise distribution data. Our analysis uses quantum machine learning (QML) circuits as case study for drawing a distinction between noisy and less noisy basis states.

Senapati, Priyabrata [Kent State University]↗
DOE OSTI2026

Technical Basis SAVY-4000® Series, 5.5G Container (Rev. 1)

The 5.5 Gallon (5.5G) SAVY-4000® nuclear material storage container is the latest in the SAVY-4000® series. The 5.5G is similar to that of a 1or 2Qt container in functionality with the exception of a larger volume deep drawn and spun form body achieved through increases in the depth and diameter of the container. Here, a technical basis using engineering equivalency analysis, calculation, and test data is presented to establish that the 5.5G SAVY-4000® Container is a DOE Manual 441.1-1 compliant container at a drop height of 9 feet (rather than the typical 12 ft of the other SAVY-4000® containers) and that a twenty-five year design life (as with the currently approved SAVY-4000® series) is justified.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Bridging the gap between molecules and materials in quantum chemistry with localized active spaces

The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.

method development↗
DOE OSTI2024

Capturing Correlation Effects in Positron Binding to Atoms and Molecules

A major challenge in contemporary electronic structure theory involves the development of methods to describe in a balanced manner the contribution of correlation effects to energy differences. This challenge can be even greater for multicomponent systems containing more than one type of quantum particle. In the present work, we describe a flexible code for carrying out self-consistent field and configuration interaction (CI) calculations on multicomponent systems and use it to generate trial wave functions for use in diffusion Monte Carlo (DMC) calculations of the positron affinity of Be, Be 2 , Be 4 , Mg, CS 2 , and benzene. The resulting positron affinities (PAs) are in good agreement with the best values from the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗