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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 OSTI2024

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Fyn–Saracatinib Complex Structure Reveals an Active State-like Conformation

Fyn is a Src-family tyrosine kinase implicated in synaptic dysfunction and neuroinflammation across multiple neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). Saracatinib (AZD0530) is a potent Src-family inhibitor that has been explored as a repurposed therapeutic; however, its clinical utility is limited by poor kinase selectivity caused by high sequence conservation within Src-family ATP-binding sites. Here, we combine surface plasmon resonance (SPR) and X-ray crystallography to define saracatinib recognition by the Fyn kinase domain (KD). SPR single-cycle kinetics shows that saracatinib binds the isolated Fyn KD and full-length Fyn with low-nanomolar affinity, whereas dasatinib binds with subnanomolar affinity and markedly slower dissociation. We determined the crystal structure of the Fyn KD-saracatinib complex at 2.22 Å resolution. The kinase adopts an active-like conformation with the DFG motif and αC-helix in the ‘in’ state and a conserved β3 αC Lys-Glu salt bridge. Saracatinib occupies the adenine and ribose pockets, and engages the hinge through direct and water-mediated hydrogen bonding while complementing a hydrophobic back pocket by van der Waals contacts. Comparison with reported saracatinib-bound structures of other kinases suggests that the active-state geometry observed for Fyn creates a pocket not observed in inactive-like complexes, providing a structural handle for designing Fyn-selective inhibitors. Comparison with all saracatinib-bound kinase co-structures currently available in the PDB (ALK2 and PKMYT1) indicates a conserved monodentate hinge binding mode but kinase-dependent αC-helix conformations, providing a structural rationale for designing Fyn-selective analogues.

AZD0530↗
NASA NTRS1987

Geometrical analysis of Cys-Cys bridges in proteins and their prediction from incomplete structural information

Analysis of C-alpha atom positions from cysteines involved in disulphide bridges in protein crystals shows that their geometric characteristics are unique with respect to other Cys-Cys, non-bridging pairs. They may be used for predicting disulphide connections in incompletely determined protein structures, such as low resolution crystallography or theoretical folding experiments. The basic unit for analysis and prediction is the 3 x 3 distance matrix for Cx positions of residues (i - 1), Cys(i), (i +1) with (j - 1), Cys(j), (j + 1). In each of its columns, row and diagonal vector--outer distances are larger than the central distance. This analysis is compared with some analytical models.

NASA Discipline Exobiology↗
NASA NTRS1993

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

NASA Discipline Number 52-20↗
NASA NTRS1992

Crystal structure of an Okazaki fragment at 2-A resolution

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Non-NASA Center↗
NASA NTRS2005

Structural and energetic consequences of mutations in a solvated hydrophobic cavity

The structural and energetic consequences of modifications to the hydrophobic cavity of interleukin 1-beta (IL-1beta) are described. Previous reports demonstrated that the entirely hydrophobic cavity of IL-1beta contains positionally disordered water. To gain a better understanding of the nature of this cavity and the water therein, a number of mutant proteins were constructed by site-directed mutagenesis, designed to result in altered hydrophobicity of the cavity. These mutations involve the replacement of specific phenylalanine residues, which circumscribe the cavity, with tyrosine, tryptophan, leucine and isoleucine. Using differential scanning calorimetry to determine the relative stabilities of the wild-type and mutant proteins, we found all of the mutants to be destabilizing. X-ray crystallography was used to identify the structural consequences of the mutations. No clear correlation between the hydrophobicities of the specific side-chains introduced and the resulting stabilities was found.

Solvents/chemistry↗
DOE OSTI2025

From cytoplasm to lumen—mapping the free pools of protein subunits of three photosynthetic complexes using quantitative mass spectrometry

The phycobilisome (PBS) captures light energy and transfers it to photosystem I (PSI) and photosystem II (PSII). Which and how many copies of protein subunits in PBSs, PSI, and PSII remain unbound in thylakoids are unknown. Here, quantitative mass spectrometry (QMS) was used to quantify substantial pools of free extrinsic subunits of PSII and PSI. Interestingly, the membrane intrinsic PsaL is 3-fold higher than PsaA/B. This scenario complements the static structures of these complexes as revealed by X-ray crystallography and cryo-EM. Furthermore, the ratios of ApcG and photoprotective OCP over PBS indicate a pool of extra ApcG. The 2.5 ratio of CpcG-PBS over CpcL-PBS improves our understanding of these light-harvesting complexes involved in energy capture and photoprotection in cyanobacteria.

cyanobacteria↗
DOE OSTI2025

The Anisotropic Adsorption of De Novo Allosteric Two‐Component Protein Fibers on Mica Surfaces

Protein adsorption at solid–liquid interfaces underlies many biomedical and materials applications, yet the mechanisms governing adsorption of proteins and their assemblies remain poorly understood. Here we investigate de novo–designed proteins that self-assemble into three fibrillar morphologies — small (S), large (L), and helical (H)—on muscovite mica. S-fibers are metastable, forming first but diminishing as L- and H-fibers develop and deposit. Adsorption of both fibers and monomers depends on fiber morphology and solvent environment, which is modulated by the substrate. The anisotropic surface features of the fiber types—long axis of S- and L-fibers and helical grooves of H-fibers—correlate with specific crystallographic directions on mica (001). S- and L-fibers align along the unique lattice axis, while the substrate-facing groove of H-fibers preferentially aligns along the remaining symmetry-related directions. Increasing potassium chloride (KCl) concentrations to molar levels alters adsorption, decreasing monomer coverage relative to fibers. These observations, interpreted through the effect of interfacial interface, indicate that ion-mediated modulation of hydration layers governs electrostatic interactions and alignment. This study reveals how coupling between protein topography, substrate crystallography, and hydration structure dictates selective adsorption and orientation of protein assemblies, offering insights for rational biomolecular material design.

AFM↗
DOE OSTI2024

Birefringent Color Filter by Layered Metal‐Organic Chalcogenides: In‐Plane Anisotropy and Odd/Even Effect

Anisotropic 2D materials are gaining interest recently as building blocks for angular‐dependent optical/electrical devices. However, the fundamental understanding of their structure‐property‐relationship is limited, which hinders further modulation of their unique characteristics via structure tailoring. Here the in‐plane structural anisotropy and the tunable optical/electrical properties of a series of radiation‐sensitive (X‐ray, e‐beam) metal‐organic chalcogenide (MOC) single crystals are comprehensively revealed with ligands of variable length/parity. Their monoclinic crystallography is determined at atomic resolution by a simple method that couples X‐ray/electron diffraction with first‐principles calculations. The in‐plane inorganic backbone of the MOCs exhibits a strong lattice anisotropy with odd/even alternations, which originates from that of the out‐of‐plane organic motifs via organic/inorganic accommodation. Such structural anisotropy is implied mechanically by the preferred orientation of crystal cleavage. It triggers a maximum ≈8 × distinction of in‐plane electrical conductivity of the semiconducting MOCs, plus a distinct birefringence (maximum Δn ≈ 0.03) with a dispersive orientation of dielectric axes, which rotate up to 25.7° from UV to visible‐light regime, inspiring an emerging pathway for color filtering via single crystal rotation. Such in‐plane optical characteristics also exhibit odd/even alternation and can be flexibly tuned by the designable out‐of‐plane ligands.

birefringence↗
DOE OSTI2025

Dislocation‐Driven Formation of Oriented Macroperiodic Metastructures of Curved Single Crystal Lattices in Glass

Abstract Single crystals fabricated in glass by localized heating can develop uniquely deformed lattices stabilized by the surrounding amorphous medium. The development of lattice curvature appears to be intrinsic to the crystal growth process in some systems, while the result of the locally changing crystallography in others. In this work, a model laser‐fabricated rotating lattice Sb 2 S 3 crystal grown in stoichiometric glass is used to demonstrate fabrication of novel macroperiodic metastructures that utilize intrinsic lattice curvature superimposed with subtle crystallographic influences. The limited availability of slip systems drives the lattice curvature magnitude to vary with crystal growth direction, maximizing for lattices aligned with the predominant Burgers vector along with corresponding increases in dislocation density. Misaligned lattice orientations form smaller secondary lattice curvatures arising from misaligned Burgers vectors with further elastic contributions. Over extended crystal growth, these secondary components align the lattice to rotate about either the <001> or <010> crystal axes forming repeating metastructures of lattice orientation with periodicity 20–160 microns in length. The mechanistic approach used in this work may be expanded to other systems with known slip systems to better understand and design macroperiodic metastructures.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Heterogeneity of the Dominant Causes of Performance Loss in End-of-Life Cathodes and Their Consequences for Direct Recycling

Recycling Li-ion batteries from electric vehicles is critical for reducing costs and supporting the development of a domestic battery supply chain. Direct recycling of cathodes, like LiNixMnyCozO2 (NMC), is attractive due to its low cost, energy use, and emissions compared to traditional recycling techniques. However, a comprehensive understanding of the active material properties at end-of-life is needed to guide direct recycling processes and the performance-dependent reuse applications. Here, NMC material from an end-of-life commercial pouch cell is characterized and bench-marked against pristine non-cycled counterparts with respect to capacity, impedance, crystallography, morphology, and microstructure to identify major degradation modes and understand variability in the end-of-life material. The spatial heterogeneity of each property throughout the cell is also quantified. While the degraded material demonstrated similar capacity as the pristine, its impedance and rate capability are severely diminished. Furthermore, samples from the periphery of the electrode layers showed more severe performance loss compared to samples extracted from central regions. The dominant culprit of performance loss is the material microstructure, where the magnitude of particle cracking showed the strongest correlation to the impedance components that are most unfavorably impacted. This work suggests severe cracks in cathode active materials are the primary challenge that direct recycling methods must overcome.

25 ENERGY STORAGE↗
DOE OSTI2025

Protein–Protein Complex Stability Controls Substrate Scope in a β‐Ketoacyl‐ACP Reductase Specific for Medium Chains

Assembly-line enzymes carry out multistep synthesis of important metabolites by using acyl carrier proteins (ACPs) to shuttle intermediates along defined sequences of active sites. Despite longstanding interest in reprogramming these systems for metabolic engineering and biosynthetic chemistry, the mechanisms underlying their reaction order remain poorly understood and difficult to control. In this work, we describe a β-ketoacyl-ACP reductase from Pseudomonas putida (PpFabG4) with an unusual selectivity for medium chains and use it to explore the molecular basis of substrate specificity in enzymes that pull intermediates from fatty acid synthesis, a common route to specialized products. X-ray crystallography shows no obvious barriers to short-chain binding. Molecular simulations and supporting mutational analyses indicate that substrate preference arises instead from a weak enzyme–ACP interaction that is stabilized by medium acyl chains but not by short chains. Indeed, mutations that strengthen this interaction for PpFabG4 or weaken it for EcFabG, an Escherichia coli β-ketoacyl-ACP reductase with a broad substrate specificity, can enhance or reduce activity on short-chain substrates by over 100-fold. Our findings show how the stability of enzyme-ACP interactions can control substrate scope in promiscuous enzymes and guide the exchange of intermediates between (and within) assembly-line systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Comparative Study of Solvatomorphs of Stryker's Reagent Using MicroED and Quantum Mechanics

Abstract The atomic position of hydrogen atoms in metal hydrides has been a long‐standing structural question in inorganic chemistry given that hydride delivery is integral to diverse chemical reactions. Microcrystal electron diffraction (microED), with it's increased sensitivity toward hydrogen atoms relative to X‐ray diffraction, offers a potential path to addressing this challenge. Herein, the first microED study of Stryker's reagent is reported, resulting in the structure of a new benzene solvate. Improved accuracy for hydrogen atom positions was obtained via a quantum crystallography (QCr) approach, Hirshfeld atom refinement (HAR). Structural and topological analysis supports edge bridging hydrides in the microED structure of a THF solvate form, consistent with previous diffraction studies. Interestingly, analysis of a new benzene solvate, discovered in this study, is consistent with mixed edge‐ and face‐bridging hydrides.

Jha, Kunal K. [Division of Chemistry &amp, Chemica↗
DOE OSTI2025

Machine Learning‐Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands

Abstract The challenge of targeting RNA with small molecules necessitates a better understanding of RNA–ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand‐induced stabilization, and how conformational changes influence gene expression pose significant difficulties for experimental investigation. This work employs a combination of computational and experimental methods to address these challenges. By integrating structure‐informed design, crystallography, and machine learning‐augmented all‐atom molecular dynamics simulations (MD), we synthesized, biophysically and biochemically characterized, and studied the dissociation of a library of small molecule activators of the 5‐aminoimidazole–4–carboxamide ribonucleotide triphosphate (ZTP) riboswitch, a ligand‐binding RNA motif that regulates bacterial gene expression. We uncovered key interaction mechanisms, revealing valuable insights into the role of ligand binding kinetics on riboswitch activation. Further, we established that ligand on‐rates determine activation potency as opposed to binding affinity and elucidated RNA structural differences, which provide mechanistic insights into the interplay of RNA structure on riboswitch activation.

Chemistry↗
DOE OSTI2024

Neptunyl Pyrrophen Complexes: Exploring Schiff Base Chemistry with Multidentate Acyclic Ligands and Transuranics

Here we report the synthesis, structure, and characterization of two novel neptunyl complexes (NpO 2 L1 and NpO 2 L2) constructed from phenylene-substituted benzyl ester bis(pyrrole)phenylenediamine (named “pyrrophen”) ligands. In both cases, the neptunium center exists in the +6 oxidation state,. As our specific interest is in exploring the chemistry of neptunium compounds containing the linear neptunyl ion (NpO 2 2+ ) through equatorially coordinating the metal by multidentate organic ligands, we have identified the differences that are likely to cause discrepancy between the two complexes by examining the ions and their coordinative environments through single-crystal X-ray crystallography, diffuse reflectance, and Raman spectroscopy. This is the first time pyrrophen has been utilized in Np chemistry and demonstrates a new platform to study 5 f electron participation and coordination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Thorium Bis‐Salophen Trimers as Anion Detectors and Binding Agents

Bis‐salophen ligands are the condensation product of a tetramine and a salicylaldehyde derivative. They feature two binding sites, both of which are tetradentate with mixed O/N donor atoms. Reaction with the ligand precursor and thorium nitrate tetrahydrate forms a 3:3 metal‐to‐ligand trimer with a ΔΔΔ‐chirality confirmed by X‐ray crystallography of a racemic single crystal. The structure has a pore in the center of the triangular structure measuring 6.22 Å at its narrowest point. This compound is air‐ and water‐stable as well as soluble in organic solvents. Here, this compound was screened with a series of tetrabutyl ammonium halide salts, and tetrabutylammonium (TBA) chloride showed the strongest binding to the complex. After the addition of 2 equivalents of TBACl, the complex and salt precipitate out of solution.

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

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Poon, Billy K.↗