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

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448–605 of μNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-μNS (448–605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-μNS (448–605) baculovirus formed rod-shaped microcrystals (5–15 µm in length) which were reconstituted in high-viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 Å resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 Å. The final data set was merged and refined to 7.0 Å resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of μNS (448–605) , the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the μNS protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring 3D leaf anatomical traits for C 4 photosynthesis: chloroplast and plasmodesmata pit field size in maize and sugarcane

Summary Volume and surface area of chloroplasts and surface area of plasmodesmata pit fields are presented for two C 4 species, maize and sugarcane, with respect to cell surface area and cell volume. Serial block face scanning electron microscopy (SBF‐SEM) and confocal laser scanning microscopy with the Airyscan system (LSM) were used. Chloroplast size estimates were much faster and easier using LSM than with SBF‐SEM; however, the results were more variable than SBF‐SEM. Mesophyll cells were lobed where chloroplasts were located, facilitating cell‐to‐cell connections while allowing for greater intercellular airspace exposure. Bundle sheath cells were cylindrical with chloroplasts arranged centrifugally. Chloroplasts occupied c. 30–50% of mesophyll cell volume, and 60–70% of bundle sheath cell volume. Roughly 2–3% of each cell surface area was covered by plasmodesmata pit fields for both bundle sheath and mesophyll cells. This work will aid future research to develop SBF‐SEM methodologies with the aim to better understand the effect of cell structure on C 4 photosynthesis.

3D leaf imaging↗
DOE OSTI2020

Ultrafast structural response to charge redistribution within a photosinthetic reaction centre

This data set contains stream files, difference maps and SVD maps obtained from data processing of time-resolved serial femtosecond crystallography measurements performed at LCLS XFEL, used to construct the images and perform the analysis published in the paper "Ultrafast structural response to charge redistribution within a photosinthetic reaction centre". Two (2) time points plus a dark state from 2015 ('a' label) as well as five (5) time points plus a dark state from 2016 ('b' label) are provided.

CXI↗
DOE OSTI2020

Mechanism and dynamics of fatty acid photodecarboxylase

The deposition contains diffraction patterns after hit-finding of time-resolved serial femtosecond crystallography measurements on fatty acid photodecarboxylase performed at LCLS XFEL (proposal ID: LT59). Five datasets are available. One dataset without pump laser excitation, labeled as "dark" and four time-resolved datasets with pump laser excitation at four different time-points labeled as "20 ps", "900 ps", "300 ns" and "2 μs". Please check the publication for more information about the datasets.

CXI↗
DOE OSTI2022

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

This dataset contains a subset of raw diffraction images for the serial femtosecond crystallography data of S1P5-ONO-5430608 complex. The diffraction data contain a strong systematic background as described in Lyapina et al. No additional background subtraction was applied to the data. In order to avoid its effects, the background subtraction implemented in CrystFEL, was applied (--rings-grad subtraction). The final stream, supplemented with this dataset, was obtained with: indexamajig 0.8.0 Respectively, the hkl file was obtained with: partialator 0.8.0

Human sphingosine-1-phosphate receptor 5 (S1P5) in↗
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 OSTI2020

Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff

Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have truly delivered on these promises. Why? SFX has many paradigm shifting techniques not seen in typical structural biology arenas, such as creating a concentrated slurry of microcrystals rather than a handful of loopable prisms worthy of a catalog photo. Then taking that slurry and high speed jetting them towards the vacuum or helium interation region to destroy less than 1% of your sample and waste the other 99. The literature is full of techniques and methods promising to cure what ails your experiment, yet as an instrument scientist will tell you –and a first author might admit after a few drinks at the conference happy hour—is that there are a lot more failures than the success we published, results may vary. We will walk through a best practices on how to prepare your sample and chose a sample delivery technique that will amerliorate your studies rather than undermine your hardwork and hopefully lead to better experimental planning and execution, inching you closer to that scientific goal and that call from Stockholm. This will be written in a more editorialized fashion and is meant to give the reader an idea of what to try or how they should be thinking. Welcome to SFX, now what?

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

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

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Herpes simplex virus and rates of cognitive decline or whole brain atrophy in the Dominantly Inherited Alzheimer Network

Abstract Objective To investigate whether herpes simplex virus type 1 (HSV‐1) infection was associated with rates of cognitive decline or whole brain atrophy among individuals from the Dominantly Inherited Alzheimer Network (DIAN). Methods Among two subsets of the DIAN cohort (age range 19.6–66.6 years; median follow‐up 3.0 years) we examined (i) rate of cognitive decline ( N = 164) using change in mini‐mental state examination (MMSE) score, (ii) rate of whole brain atrophy ( N = 149), derived from serial MR imaging, calculated using the boundary shift integral (BSI) method. HSV‐1 antibodies were assayed in baseline sera collected from 2009–2015. Linear mixed‐effects models were used to compare outcomes by HSV‐1 seropositivity and high HSV‐1 IgG titres/IgM status. Results There was no association between baseline HSV‐1 seropositivity and rates of cognitive decline or whole brain atrophy. Having high HSV‐1 IgG titres/IgM was associated with a slightly greater decline in MMSE points per year (difference in slope − 0.365, 95% CI: −0.958 to −0.072), but not with rate of whole brain atrophy. Symptomatic mutation carriers declined fastest on both MMSE and BSI measures, however, this was not influenced by HSV‐1. Among asymptomatic mutation carriers, rates of decline on MMSE and BSI were slightly greater among those who were HSV‐1 seronegative. Among mutation‐negative individuals, no differences were seen by HSV‐1. Stratifying by APOE4 status yielded inconsistent results. Interpretation We found no evidence for a major role of HSV‐1, measured by serum antibodies, in cognitive decline or whole brain atrophy among individuals at high risk of early‐onset AD.

Warren‐Gash, Charlotte↗
DOE OSTI2024

Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates

X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.

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

A Three-in-One Hybrid Strategy for High-Performance Semiconducting Polymers Processed from Anisole

The development of semiconducting polymers with good processability in green solvents and competitive electrical performance is essential for realizing sustainable large-scale manufacturing and commercialization of organic electronics. A major obstacle is the processability-performance dichotomy that is dictated by the lack of ideal building blocks with balanced polarity, solubility, electronic structures, and molecular conformation. Herein, through the integration of donor, quinoid and acceptor units, an unprecedented building block, namely TQBT, is introduced for constructing a serial of conjugated polymers. The TQBT, distinct in non-symmetric structure and high dipole moment, imparts enhanced solubility in anisole—a green solvent—to the polymer TQBT-T. Furthermore, PTQBT-T possess a highly rigid and planar backbone owing to the nearly coplanar geometry and quinoidal nature of TQBT, resulting in strong aggregation in solution and localized aggregates in film. Remarkably, PTQBT-T films spuncast from anisole exhibit a hole mobility of 2.30 cm 2 V -1 s -1 , which is record high for green solvent-processable semiconducting polymers via spin-coating, together with commendable operational and storage stability. The hybrid building block emerges as a pioneering electroactive unit, shedding light on future design strategies in high-performance semiconducting polymers compatible with green processing and marking a significant stride towards ecofriendly organic electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Indirect Liftoff Mechanism for High‐Throughput, Single‐Source Laser Scribing for Perovskite Solar Modules

A high‐throughput, single‐source laser scribing method exploiting a transparent conducting oxide (TCO) indirect liftoff mechanism is developed to produce serially interconnected perovskite solar modules. The TCO‐based indirect liftoff mechanism relies solely on laser absorption in the front transparent electrode material reducing thermal damage to the overlying layers and allowing for fast scribing speeds with low‐cost μs‐pulse duration fiber laser systems. Minimal resistive power losses are observed with the method compared to conventional ablative laser scribes, maintaining the power conversion efficiencies of small‐area devices (≈0.2 cm 2 ) across significantly larger deposition areas (≈1 cm 2 ). Finally, demonstrating > 3 m s −1 processing speeds, TCO‐based liftoff provides the highest throughput laser scribing method for thin‐film photovoltaic devices produced on glass/TCO substrates, capable of processing large‐area perovskite solar modules at a manufacturing scale.

14 SOLAR ENERGY↗
DOE OSTI2024

Large language model evaluation for high–performance computing software development

We apply AI-assisted large language model (LLM) capabilities of GPT-3 targeting high-performance computing (HPC) kernels for (i) code generation, and (ii) auto-parallelization of serial code in C ++, Fortran, Python and Julia. Our scope includes the following fundamental numerical kernels: AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG, and language/programming models: (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). Kernel implementations are generated using GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code given simple + + prompt variants. To quantify and compare the generated results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. For auto-parallelization, we use ChatGPT interactively giving simple prompts as in a dialogue with another human including simple “prompt engineering” follow ups. Results suggest that correct outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding language keywords, while Julia prompts perform acceptably well for its Threads and CUDA.jl programming models. Finally, we expect to provide an initial quantifiable point of reference for code generation in each programming model using a state-of-the-art LLM. Overall, understanding the convergence of LLMs, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Endowing Polythioester Vitrimer with Intrinsic Crystallinity and Chemical Recyclability

Abstract Technologically important thermosets face a long‐standing end‐of‐life (EoL) problem of non‐reprocessability, a more sustainable solution of which has resolved to nascent vitrimers that can merge the robust material properties of thermosets and the reprocessability of thermoplastics. However, the lifecycle of vitrimers is still finite, as they often suffer from significant deterioration of mechanical performance following multiple reprocessing cycles, analogous to mechanical recycling, and they often show undesired creep under working conditions. To address these two key limitations, we have developed a cross‐linked semi‐crystalline polythioester with both dynamic covalent bonds and intrinsic crystallinity and chemical recyclability, affording a vitrimeric system that exhibits not only reprocessability and crystallinity‐restricted creep but also complete chemical recyclability to initial monomer by catalyzed depolymerization in solution or bulk. Therefore, reported herein is an “infinite” vitrimer system that is empowered with a facile closed‐loop EoL option once serial reprocessing deteriorates performance and the material can no longer meet the application requirements. Specifically, the polythioester vitrimer was constructed by copolymerization of a bicyclic thioester with a bis‐dithiolane, producing dynamically cross‐linked polythioesters with excellent property tunability, from amorphous to semi‐crystalline states and melting transition temperatures from 91 to 178 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Speedup of UEDGE Parameter Scans Using Machine-Learning Optimized OpenMP Parallelization and a Continuation Solver

This article presents the OpenMP parallelization of the preconditioning Jacobian assembly and right‐hand side residual evaluation in UEDGE. A continuation algorithm, utilizing the internal NKSOL implicit Jacobian‐Free Newton‐Krylov solver to efficiently scan physical parameters, is also presented. The implemented parallelization reduces the computational time for a benchmark scan run on 32 threads by compared to the serial version when using trained random forest regression models to identify the optimal decomposition of the system of equations. Random forest regression models applied to the UEDGE time‐dependent and continuation solver algorithms did not yield meaningful improvement in computational performance. A benchmark DIII‐D gas injection rate scan in the 0.35–0.75 kA interval, performed on a test cluster using the parallelized code and continuation solver, produced 1066 steady‐state solutions with a 22 s average wall‐clock computational time per steady‐state solution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Weighted relaxation for multigrid reduction in time

Current trends in computer architectures now mean that faster computation speed must come primarily from increased concurrency, not faster clock speeds, which are stagnating. Thus, this situation creates bottlenecks for serial algorithms, including the well-known bottleneck for sequential time-integration, where each individual time-value (i.e., time-step) is computed sequentially. One approach to alleviate this and achieve parallelism in time is with multigrid. Here, in this work, we consider multigrid-reduction-in-time (MGRIT), a multilevel method applied to the time dimension that computes multiple time-steps in parallel. Like all multigrid methods, MGRIT relies on the complementary relationship between relaxation on a fine-grid and a correction from the coarse grid to solve the problem. All current MGRIT implementations are based on unweighted-Jacobi relaxation; here we introduce the concept of weighted relaxation to MGRIT. We derive new convergence bounds for weighted relaxation, and use this analysis to guide the selection of relaxation weights. Numerical results then demonstrate that by choosing appropriate non-unitary relaxation weights, one can achieve faster convergence rates and lower iteration counts for MGRIT when compared with unweighted relaxation. In most cases, weighted relaxation yields a 10%–20% saving in iterations, which is significant when using large high-performance computers. For A-stable integration schemes, results also illustrate that under-relaxation can restore convergence in some cases where unweighted relaxation is not convergent.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds

Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis.

Kotei, Patience A.↗