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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases

N 6 -methyladenosine (m 6 A) is a prevalent, reversible chemical modification of functional RNAs and is important for central events in biology. The core m 6 A writers are Mettl3 and Mettl14, which both contain methyltransferase domains. How Mettl3 and Mettl14 cooperate to catalyze methylation of adenosines has remained elusive. Here, we present crystal structures of the complex of Mettl3/Mettl14 methyltransferase domains in apo form as well as with bound S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) in the catalytic site. We determine that the heterodimeric complex of methyltransferase domains, combined with CCCH motifs, constitutes the minimally required regions for creating m 6 A modifications in vitro. We also show that Mettl3 is the catalytically active subunit, while Mettl14 plays a structural role critical for substrate recognition. Our model provides a molecular explanation for why certain mutations of Mettl3 and Mettl14 lead to impaired function of the methyltransferase complex.

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

Contactless diagnostics of biophysical parameters of skin and blood on the basis of approximating functions for radiation fluxes scattered by skin

Approximating expressions are derived to calculate spectral and spatial characteristics of diffuse reflection of light from a two-layer medium mimicking human skin. The effectiveness of the use of these expressions in the optical diagnosis of skin biophysical parameters (tissue scattering parameters, concentration of melanin in the epidermis, concentration of total haemoglobin and bilirubin in the tissues of the dermis) and content of haemoglobin derivatives in blood (oxy-, deoxy-, met-, carboxy- and sulfhaemoglobin) is analysed numerically. The methods are proposed to determine in realtime these parameters without contact of the measuring instrument with the patient's body. (biophotonics)

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Estimating the Effectiveness of Personnel Management at Aviation Enterprises

Assessment of the effectiveness of personnel management at the United Aircraft Corporation (UAC) is considered. Three groups of personnel-management functions are identified. Their significance is analyzed in the light of the organization’s life cycle. Assessment of the outsourcing of functions on the basis of functional and cost analysis is proposed.

14 SOLAR ENERGY↗
DOE OSTI2012

The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1

Proper formation of protein phosphatase 2A (PP2A) holoenzymes is essential for the fitness of all eukaryotic cells. Carboxyl methylation of the PP2A catalytic subunit plays a critical role in regulating holoenzyme assembly; methylation is catalyzed by PP2A-specific methyltransferase LCMT-1, an enzyme required for cell survival. We determined crystal structures of human LCMT-1 in isolation and in complex with PP2A stabilized by a cofactor mimic. The structures show that the LCMT-1 active-site pocket recognizes the carboxyl terminus of PP2A, and, interestingly, the PP2A active site makes extensive contacts to LCMT-1. We demonstrated that activation of the PP2A active site stimulates methylation, suggesting a mechanism for efficient conversion of activated PP2A into substrate-specific holoenzymes, thus minimizing unregulated phosphatase activity or formation of inactive holoenzymes. A dominant-negative LCMT-1 mutant attenuates the cell cycle without causing cell death, likely by inhibiting uncontrolled phosphatase activity. Our studies suggested mechanisms of LCMT-1 in tight control of PP2A function, important for the cell cycle and cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Three-dimensional reconstruction of x-ray emission volumes in magnetized liner inertial fusion from sparse projection data using a learned basis

The ability to visualize x-ray and neutron emission from fusion plasmas in 3D is critical to understand the origin of the complex shapes of the plasmas in experiments. Unfortunately, this remains challenging in experiments that study a fusion concept known as Magnetized Liner Inertial Fusion (MagLIF) due to a small number of available diagnostic views. Here, we present a basis function-expansion approach to reconstruct MagLIF stagnation plasmas from a sparse set of x-ray emission images. A set of natural basis functions is “learned” from training volumes containing quasi-helical structures whose projections are qualitatively similar to those observed in experimental images. Tests on several known volumes demonstrate that the learned basis outperforms both a cylindrical harmonic basis and a simple voxel basis with additional regularization, according to several metrics. Two-view reconstructions with the learned basis can estimate emission volumes to within 11% and those with three views recover morphology to a high degree of accuracy. The technique is applied to experimental data, producing the first 3D reconstruction of a MagLIF stagnation column from multiple views, providing additional indications of liner instabilities imprinting onto the emitting plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number L max = (l,m) max , while scattering matrices, which determine spectral properties, are truncated at L tr = (l,m) tr where phase shifts δl>l tr are negligible. Historically, L max is set equal to L tr , which is correct for large enough L max but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for L max > L tr with δl>l tr set to zero [Zhang and Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R 3 process with rank N(l tr + 1) 2 ] and includes higher-L contributions via linear algebra [R 2 process with rank N(l max +1) 2 ]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L1 0 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus L max for a given L tr .

36 MATERIALS SCIENCE↗
DOE OSTI2015

DGDFT: A massively parallel method for large scale density functional theory calculations

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Consistent structures and interactions by density functional theory with small atomic orbital basis sets

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust “high-speed” computational tool in theoretical chemistry and physics.

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

Comparing (stochastic-selection) ab initio multiple spawning with trajectory surface hopping for the photodynamics of cyclopropanone, fulvene, and dithiane

Ab Initio Multiple Spawning (AIMS) simulates the excited-state dynamics of molecular systems by representing nuclear wavepackets in a basis of coupled traveling Gaussian functions, called trajectory basis functions (TBFs). New TBFs are spawned when nuclear wavepackets enter regions of strong nonadiabaticity, permitting the description of non-Born–Oppenheimer processes. The spawning algorithm is simultaneously the blessing and the curse of the AIMS method: it allows for an accurate description of the transfer of nuclear amplitude between different electronic states, but it also dramatically increases the computational cost of the AIMS dynamics as all TBFs are coupled. Recently, a strategy coined stochastic-selection AIMS (SSAIMS) was devised to limit the ever-growing number of TBFs and tested on simple molecules. In this work, we use the photodynamics of three different molecules—cyclopropanone, fulvene, and 1,2-dithiane—to investigate (i) the potential of SSAIMS to reproduce reference AIMS results for challenging nonadiabatic dynamics, (ii) the compromise achieved by SSAIMS in obtaining accurate results while using the smallest average number of TBFs as possible, and (iii) the performance of SSAIMS in comparison to the mixed quantum/classical method trajectory surface hopping (TSH)—both in terms of its accuracy and computational cost. We show that SSAIMS can accurately reproduce the AIMS results for the three molecules considered at a much cheaper computational cost, often close to that of TSH. We deduce from these tests that an overlap-based criterion for the stochastic-selection process leads to the best agreement with the reference AIMS dynamics for the smallest average number of TBFs.

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

Modeling and characterizing anisotropic inclusion orientation in heterogeneous material via directional cluster functions and stochastic microstructure reconstruction

We present a framework to model and characterize the microstructure of heterogeneous materials with anisotropic inclusions of secondary phases based on the directional correlation functions of the inclusions. Specifically, we have devised an efficient method to incorporate both directional two-point correlation functions S{sub 2} and directional two-point cluster functions C{sub 2} that contain non-trivial topological connectedness information into the simulated annealing microstructure reconstruction procedure. Our framework is applied to model an anisotropic aluminum alloy and the accuracy of the reconstructed structural models is assessed by quantitative comparison with the actual microstructure obtained via x-ray tomography. We show that incorporation of directional clustering information via C{sub 2} significantly improves the accuracy of the reconstruction. In addition, a set of analytical “basis” correlation functions are introduced to approximate the actual S{sub 2} and C{sub 2} of the material. With the proper choice of basis functions, the anisotropic microstructure can be represented by a handful of parameters including the effective linear sizes of the iron-rich and silicon-rich inclusions along three orthogonal directions. This provides a general and efficient means for heterogeneous material modeling that enables one to significantly reduce the data set required to characterize the anisotropic microstructure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Discrete spherical harmonic functions for texture representation and analysis

A basis of discrete harmonic functions for efficient representation and analysis of crystallographic texture is presented. Discrete harmonics are a numerical representation of the harmonics on the sphere. A finite element formulation is utilized to calculate these orthonormal basis functions, which provides several advantageous features for quantitative texture analysis. These include high-precision numerical integration, a simple implementation of the non-negativity constraint and computational efficiency. Simple examples of pole figure and texture interpolation and of Fourier filtering using these basis sets are presented.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Bayes goes fast: Uncertainty quantification for a covariant energy density functional emulated by the reduced basis method

A covariant energy density functional is calibrated using a principled Bayesian statistical framework informed by experimental binding energies and charge radii of several magic and semi-magic nuclei. The Bayesian sampling required for the calibration is enabled by the emulation of the high-fidelity model through the implementation of a reduced basis method (RBM)—a set of dimensionality reduction techniques that can speed up demanding calculations involving partial differential equations by several orders of magnitude. The RBM emulator we build—using only 100 evaluations of the high-fidelity model—is able to accurately reproduce the model calculations in tens of milliseconds on a personal computer, an increase in speed of nearly a factor of 3,300 when compared to the original solver. Besides the analysis of the posterior distribution of parameters, we present model calculations for masses and radii with properly estimated uncertainties. We also analyze the model correlation between the slope of the symmetry energy L and the neutron skin of 48 Ca and 208 Pb. The straightforward implementation and outstanding performance of the RBM makes it an ideal tool for assisting the nuclear theory community in providing reliable estimates with properly quantified uncertainties of physical observables. Such uncertainty quantification tools will become essential given the expected abundance of data from the recently inaugurated and future experimental and observational facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Global optimization of harmonic oscillator basis in covariant density functional theory

The present investigation focuses on the improvement of the accuracy of the description of binding energies within moderately sized fermionic basis. Using the solutions corresponding to infinite fermionic basis it was shown that in the case of meson exchange (ME) covariant energy density functionals (CEDFs) the global accuracy of the description of binding energies in the finite $N_F$ = 16 - 20 bases can be drastically (by a factor ranging from ~3 up to ~9 dependent on the functional and $N_F$) improved by a global optimization of oscillator frequency of the basis. This is a consequence of the unique feature of the ME functionals in which with increasing fermionic basis size fermionic and mesonic energies approach the exact (infinite basis) solution from above and below, respectively. As a consequence, an optimal oscillator frequency $\hbar\omega_0$ of the basis can be defined which provides an accurate reproduction of exact total binding energies by the ones calculated in truncated basis. This leads to a very high accuracy of the calculations in moderately sized $N_F=20$ basis when mass dependent oscillator frequency is used: global rms differences $\delta B_{rms}$ between the binding energies calculated in infinite and truncated bases are only 0.025 MeV and 0.031 MeV for the NL5(Z) and DD-MEZ functionals, respectively. Optimized values of the oscillator frequency $\hbar\omega_0$ are provided for three major classes of CEDFs, i.e. for density dependent meson exchange functionals, nonlinear meson exchange ones and point coupling functionals.

Binding energy & masses↗
DOE OSTI2013

Feasibility of kilovoltage x-ray energy modulation by gaseous media and its application in contrast-enhanced radiotherapy

Purpose: To present a method to modulate the energy contents of a kilovoltage x-ray beam that makes use of a gas as the modulating medium. The method is capable of producing arbitrary x-ray spectra by varying the pressure of the modulating gas and the peak kilovoltage (kVp) of the x-ray beams whose energy is being modulated.Methods: An aluminum chamber was machined with a 0.5 cm wall thickness, designed to withstand pressures of more than 80 atm. A pressure sensor and electrovalves were used to monitor and regulate the gas pressure. Argon was used as the modulating gas. A CdTe spectrometer was used to measure x-ray spectra for different combinations of kVp and gas pressure, thus obtaining a set of basis x-ray functions. An arbitrary x-ray spectrum can then be formed by the linear combination of such basis functions. In order to show one possible application of the modulation method, a contrast-enhanced radiotherapy prostate treatment was optimized with respect to the x-ray beam energy, without restrictions on the possible shape of the resultant x-ray spectra.Results: The x-ray spectra basis functions obtained display a smooth and gradual variation of their average energy as a function of the gas pressure for a given kVp, sometimes in the order of 1 or 2 keV. This gradual variation would be difficult to obtain with a conventional aluminum or copper filters, as the change in thickness necessary to reproduce the data presented would be in the order of micrometers, making necessary the use of a large number of such filters. Using the modulation method presented here, the authors were able to reconstruct the optimized x-ray spectra from the measured basis functions, for different optimization objectives.Conclusions: A method has been developed that allows for the controlled modulation of the energy contents of kilovoltage x-ray spectra. The method has been shown to be able to reproduce spectra of arbitrary shape, such as those obtained from the optimization of contrast-enhanced radiotherapy. The method may have other applications as well, such as in the precise matching of diagnostic x-ray catalog spectra.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Non-homogeneous solutions of a Coulomb Schrödinger equation as basis set for scattering problems

We introduce and study two-body Quasi Sturmian functions which are proposed as basis functions for applications in three-body scattering problems. They are solutions of a two-body non-homogeneous Schrödinger equation. We present different analytic expressions, including asymptotic behaviors, for the pure Coulomb potential with a driven term involving either Slater-type or Laguerre-type orbitals. The efficiency of Quasi Sturmian functions as basis set is numerically illustrated through a two-body scattering problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Accurate Hellmann–Feynman forces from density functional calculations with augmented Gaussian basis sets

The Hellmann–Feynman (HF) theorem provides a way to compute forces directly from the electron density, enabling efficient force calculations for large systems through machine learning (ML) models for the electron density. The main issue holding back the general acceptance of the HF approach for atom-centered basis sets is the well-known Pulay force which, if naively discarded, typically constitutes an error upward of 10 eV/Å in forces. In this work, we demonstrate that if a suitably augmented Gaussian basis set is used for density functional calculations, the Pulay force can be suppressed, and HF forces can be computed as accurately as analytical forces with state-of-the-art basis sets, allowing geometry optimization and molecular dynamics to be reliably performed with HF forces. Our results pave a clear path forward for the accurate and efficient simulation of large systems using ML densities and the HF theorem.

Pathak, Shivesh (ORCID:0000000172798195)↗