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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Molecular beam epitaxy and crystal structure of majority a -plane-oriented and substrate-strained Mn 3 Sn thin films grown directly on sapphire (0001)

The Kagome antiferromagnet Mn 3 Sn has garnered much attention due to the presence of exciting properties such as anomalous Hall and Nernst effects. This paper discusses the synthesis of crystalline Mn 3 Sn thin films, prepared on Al 2 O 3 (0001) substrates at 453 ± 5°C using molecular beam epitaxy. The growth is monitored in situ using reflection high energy electron diffraction and measured ex situ using x-ray diffraction, Rutherford back-scattering, and cross-sectional scanning transmission electron microscopy. Our analysis shows the in-plane lattice constants of a 1,M = 4.117 ± 0.027 Å and a 2,M = 4.943 ± 0.033 Å, which is a very unexpected result when compared to the bulk a-plane Mn 3 Sn. This indicates a strain in the film and makes it challenging to provide a straightforward explanation. In an effort to explain our results, we discuss two possible orientation relationships between the Mn 3 Sn films and the sapphire substrates. Samples prepared under these conditions appear to have smooth surfaces locally, but overall the film has a 3D island morphology. First-principles calculations provide atomic models of the Mn 3 Sn (112¯0) lattice on Al 2 O 3 (0001) high symmetry sites, indicating that the L3-R90° is the most stable configuration. A detailed discussion of the experimental data and theoretical results, as well as strain effects, is provided.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Multielectronic and multiatomic effects in the U O 4,5 x-ray absorption spectroscopy of uranium dioxide

In order to explain all of the spectral features observed in the U O 4,5 x-ray absorption spectrum of uranium dioxide (UO 2 ), it is necessary to include both multielectron effects and multiatomic effects. The 5d (core hole)-5f (electron) angular momentum coupling that gives rise to the giant resonance has been treated within ligand field density functional theory, and the electron scattering that generates the extended x-ray absorption fine structure has been included via the spectral simulation program FEFF: both within a UO 8 fluorite cluster picture. An atomic model is insufficient to explain all of the observed spectral features.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Radiation dose calculations for CT scans with tube current modulation using the approach to equilibrium function

Purpose: The approach to equilibrium function has been used previously to calculate the radiation dose to a shift-invariant medium undergoing CT scans with constant tube current [Li, Zhang, and Liu, Med. Phys. 39, 5347–5352 (2012)]. The authors have adapted this method to CT scans with tube current modulation (TCM). Methods: For a scan with variable tube current, the scan range was divided into multiple subscan ranges, each with a nearly constant tube current. Then the dose calculation algorithm presented previously was applied. For a clinical CT scan series that presented tube current per slice, the authors adopted an efficient approach that computed the longitudinal dose distribution for one scan length equal to the slice thickness, which center was at z = 0. The cumulative dose at a specific point was a summation of the contributions from all slices and the overscan. Results: The dose calculations performed for a total of four constant and variable tube current distributions agreed with the published results of Dixon and Boone [Med. Phys. 40, 111920 (14pp.) (2013)]. For an abdomen/pelvis scan of an anthropomorphic phantom (model ATOM 701-B, CIRS, Inc., VA) on a GE Lightspeed Pro 16 scanner with 120 kV, N × T = 20 mm, pitch = 1.375, z axis current modulation (auto mA), and angular current modulation (smart mA), dose measurements were performed using two lines of optically stimulated luminescence dosimeters, one of which was placed near the phantom center and the other on the surface. Dose calculations were performed on the central and peripheral axes of a cylinder containing water, whose cross-sectional mass was about equal to that of the ATOM phantom in its abdominal region, and the results agreed with the measurements within 28.4%. Conclusions: The described method provides an effective approach that takes into account subject size, scan length, and constant or variable tube current to evaluate CT dose to a shift-invariant medium. For a clinical CT scan, dose calculations may be performed with a water-containing cylinder whose cross-sectional mass is equal to that of the subject. This method has the potential to substantially improve evaluations of patient dose from clinical CT scans, compared to CTDI{sub vol}, size-specific dose estimate (SSDE), or the dose evaluated for a TCM scan with a constant tube current equal to the average tube current of the TCM scan.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

TU-F-CAMPUS-T-02: Risk Assessment of Scattered Neutrons for a Fetus From Proton Therapy of a Brain Tumor During Pregnancy

Purpose: To determine the scattered neutron dose and the resulting risk for a fetus from proton therapy for brain tumors during pregnancy. Methods: Using the Monte Carlo platform TOPAS, the ICRP reference parameters based anthropomorphic pregnancy phantoms for three stages (3-, 6-, 9-month) were applied to evaluate the scattered neutron dose and dose equivalent. To calculate the dose equivalent, organ specific linear energy transfer (LET) based quality factor was used. Treatment plans from both passive scattering (PS) and pencil beam scanning (PBS) methods were considered in this study. Results: For pencil beam scanning, the neutron dose equivalent in the soft tissue of the fetus increases from 1.53x10−{sup 3} to 2.84x10−{sup 3} mSv per treatment Gy with increasing stage of gestation. This is due to scattered neutrons from the patient as the main contaminant source in PBS and a decrease in distance between the soft tissue of the fetus and GTV with increasing stage of gestation. For passive scattering, neutron dose equivalent to the soft tissue of the fetus shows a decrease from 0.17 to 0.13 mSv per treatment Gy in different stages, while the dose to the brain shows little difference around 0.18 mSv per treatment Gy because scattered neutrons from the treatment head contribute predominantly in passive scattering. Conclusion: The results show that the neutron dose to the fetus assuming a prescribed dose of 52.2 Gy is negligible for PBS, and is comparable to the scattered dose (0–10 mSv) from a head and neck CT scan for PS. It can be concluded that the dose to fetus is far lower than the thresholds of malformation, SMR and lethal death. The excess relative risk of childhood cancer induction would be increased by 0.48 and 0.103 using the Oxford Survey of Childhood Cancers and Japanese atomic model, respectively. Changran Geng is supported by the Chinese Scholarship Council (CSC) and the National Natural Science Foundation of China (Grant No. 11475087)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Crystal Structure of the Human Astrovirus Capsid Protein

Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ~34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP90 71–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP90 71–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP90 71–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP90 71–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

An Optimization-based Atomistic-to-Continuum Coupling Method

In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally, we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Multigrid based First-Principles Molecular Dynamics

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Fattebert, Jean-Luc↗
DOE OSTI2013

NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field (ALCF-2 Early Science Program Technical Report)

Large-scale Molecular dynamics (MD) simulation based on atomic models provide a powerful tool to understand the structure-dynamics-function relationships of important biological systems. Recent advances in computing power, especially in supercomputer, make MD simulation more and more popular in modern scientific community. However, the power of classical MD simulation has been limited mainly by the accuracy of the potential energy function and the efficiency of the dynamic algorithm enabling the adequate configurational sampling. This Early Science Project is aimed to make MD simulation method go beyond current limit using the leadership supercomputer Blue Gene/Q Mira. To address the issue of potential energy accuracy, classical Drude oscillator is developed to take into account the electronic polarizability in molecular systems. In order to develop and test the Drude polarizable force field for biomolecules, extensive MD simulations of typical polypeptides, lipids are needed. This requires efficient dynamic sampling algorithm that allows fast sampling. The sampling issue can be addressed by using advanced strategies based on multiple copies in order to enhance the sampling efficiency of brute-force MD. One such method is called replica-exchange MD (REMD).

Roux, Benoit↗
DOE OSTI2023

Boundary, SOL, and Divertor Physics Studies on TCV (Final Report for Research Funded by DoE Award DE-SC0020327)

Research supported under this grant was organized around two diagnostic systems installed on the TCV tokamak located at EPFL in Lausanne, Switzerland: Multi-Spectral Imaging (MSI) and Gas-Puff Imaging (GPI). MSI monitors 2-d time-history images of up to 10 spectral lines, in the visible, using identical views for all wavelengths. The primary application of MSI is to infer 2-d time histories of electron temperature and density in the Scrape-Off-Layer (SOL) of diverted plasmas, utilizing ratios of emission from multiple neutral helium lines. The atomic models are validated against 1-d Thomson scattering measurements. SOL density and temperature maps are analyzed to infer divertor dynamics, including particle and power flows, for a variety of divertor configurations, and specifically as flux expansion along the long-legged outboard divertor is systematically varied. GPI is used to measure details of edge fluctuations in the SOL, particularly as a function of plasma triangularity (δ), including both positive and negative δ. A threshold is found, whereby for δ<-0.3, edge turbulence in the far SOL is completely suppressed. Dynamics of the filamentary turbulence was also analyzed using advance machine learning techniques. Research in support of four PhD theses was carried out within the scope of this Award, including 2 at MIT and 2 at EPFL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Polymers in Deep Eutectic Solvents

The project investigated the behavior of polymers in ionic liquids such as deep eutectic solvents using an array of techniques. These included the development of atomistic force fields, coarse graining these force fields to the united atom level, large scale molecular dynamics (MD) simulations using new thermostat algorithms, and machine learning (ML) methods for the phase behavior. The project demonstrated the feasibility and accuracy of first principles force fields for ionic liquids, deep-eutectic solvents, and urea-water mixtures. A novel hierarchical coarse graining method was then used to develop accurate and efficient united-atom models, using which microsecond simulations were performed for polymers in ionic liquids. These simulations were in quantitative agreement with experiment, thus resolving previous controversies. Methods were also developed to obtain the potential of mean force between complex ions in solution. Finally, supervised ML methods were developed for the phase behavior of polymers in ionic liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI1968

Nuclear Physics Made Very, Very Easy

The fundamental approach to nuclear physics was prepared to introduce basic reactor principles to various groups of non-nuclear technical personnel associated with NERVA Test Operations. NERVA Test Operations functions as the field test group for the Nuclear Rocket Engine Program. Nuclear Engine for Rocket Vehicle Application (NERVA) program is the combined efforts of Aerojet-General Corporation as prime contractor, and Westinghouse Astronuclear Laboratory as the major subcontractor, for the assembly and testing of nuclear rocket engines. Development of the NERVA Program is under the direction of the Space Nuclear Propulsion Office, a joint agency of the U. S. Atomic Energy Commission and the National Aeronautics and Space Administration. This report is being reprinted for use in the U. S. Atomic Energy Commission and National Aeronautics and Space Administration educational and technology utilization programs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

Ultra-metal-poor Stars: Spectroscopic Determination of Stellar Atmospheric Parameters Using Iron Non-LTE Line Abundances

We present new ultra-metal-poor stars parameters with [Fe/H] < −4.0 based on line-by-line non-local thermodynamic equilibrium (NLTE) abundances using an up-to-date iron model atom with a new recipe for non-elastic hydrogen collision rates. We study the departures from LTE in their atmospheric parameters and show that they can grow up to ∼1.00 dex in [Fe/H], ∼150 K in T{sub eff} and ∼0.5 dex in log g toward the lowest metallicities. Accurate NLTE atmospheric stellar parameters, in particular [Fe/H] being significantly higher, are the first step to eventually providing full NLTE abundance patterns that can be compared with Population III supernova nucleosynthesis yields to derive properties of the first stars. Overall, this maximizes the potential of these likely second-generation stars to investigate the early universe and how the chemical elements were formed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation

Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing atomic models for no-nucleotide and ATP states of the monomeric kinesin motor domain on microtubules from cryo-EM reconstructions at 5–6 Å resolution. By comparing these models with existing X-ray structures of ADP-bound kinesin, we infer a mechanistic scheme in which microtubule attachment, mediated by a universally conserved ‘linchpin’ residue in kinesin (N255), triggers a clamshell opening of the nucleotide cleft and accompanying release of ADP. Binding of ATP re-closes the cleft in a manner that tightly couples to translocation of cargo, via kinesin's ‘neck linker’ element. These structural transitions are reminiscent of the analogous nucleotide-exchange steps in the myosin and F1-ATPase motors and inform how the two heads of a kinesin dimer ‘gate’ each other to promote coordinated stepping along microtubules.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2015

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

43 PARTICLE ACCELERATORS↗