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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

What is ab initio in nuclear theory?

Ab initio has been used as a label in nuclear theory for over two decades. Its meaning has evolved and broadened over the years. We present our interpretation, briefly review its historical use, and discuss its present-day relation to theoretical uncertainty quantification.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Tidal response of preliminary Jupiter model

In anticipation of improved observational data for Jupiter’s gravitational field, from the Juno spacecraft, we predict the static tidal response for a variety of Jupiter interior models based on ab initio computer simulations of hydrogen–helium mixtures. We calculate hydrostatic-equilibrium gravity terms, using the non-perturbative concentric Maclaurin Spheroid method that eliminates lengthy expansions used in the theory of figures. Our method captures terms arising from the coupled tidal and rotational perturbations, which we find to be important for a rapidly rotating planet like Jupiter. Our predicted static tidal Love number, k{sub 2}=0.5900, is ∼10% larger than previous estimates. The value is, as expected, highly correlated with the zonal harmonic coefficient J {sub 2}, and is thus nearly constant when plausible changes are made to the interior structure while holding J {sub 2} fixed at the observed value. We note that the predicted static k {sub 2} might change, due to Jupiter’s dynamical response to the Galilean moons, and find reasons to argue that the change may be detectable—although we do not present here a theory of dynamical tides for highly oblate Jovian planets. An accurate model of Jupiter’s tidal response will be essential for interpreting Juno observations and identifying tidal signals from effects of other interior dynamics of Jupiter’s gravitational field.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2014

Ab Initio Modeling of Molecular Radiation

Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

spectroscopy↗
NASA NTRS2014

Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields

The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments.

Astrochemistry↗
DOE OSTI2024

Scalable bottom-up synthesis of Co-Ni–doped graphene

Introducing heteroatoms into graphene is a powerful strategy to modulate its catalytic, electronic, and magnetic properties. At variance with the cases of nitrogen (N)– and boron (B)–doped graphene, a scalable method for incorporating transition metal atoms in the carbon (C) mesh is currently lacking, limiting the applicative interest of model system studies. This work presents a during-growth synthesis enabling the incorporation of cobalt (Co) alongside nickel (Ni) atoms in graphene on a Ni(111) substrate. Single atoms are covalently stabilized within graphene double vacancies, with a Co load ranging from 0.07 to 0.22% relative to C atoms, controllable by synthesis parameters. Structural characterization involves variable-temperature scanning tunneling microscopy and ab initio calculations. The Co- and Ni-codoped layer is transferred onto a transmission electron microscopy grid, confirming stability through scanning transmission electron microscopy and electron energy loss spectroscopy. This method holds promise for applications in spintronics, gas sensing, electrochemistry and catalysis, and potential extension to graphene incorporation of similar metals.

Science & Technology - Other Topics↗
DOE OSTI2014

Potential energy curves for the ground and low-lying excited states of CuAg

The ground and low-lying excited states of heteronuclear diatomic CuAg are examined by multi-reference configuration interaction (MRCI) method. Relativistic effects were treated and probed in two steps. Scalar terms were considered using the spin-free DKH Hamiltonian as a priori and spin-orbit coupling was calculated perturbatively via the spin-orbit terms of the Breit-Pauli Hamiltonian based on MRCI wavefunctions. Potential energy curves of the spin-free states and their corresponding Ω components correlating with the separated atom limits {sup 2}S(Cu) + {sup 2}S(Ag) and {sup 2}D(Cu) + {sup 2}S(Ag) are obtained. The results are in fine agreement with the experimental measurements and tentative conclusions for the ion-pair B0{sup +} state are confirmed by our theoretical calculations. Illustrative results are presented to reveal the relative importance and magnitude of the scalar and spin-orbit effects on the spectroscopic properties of this molecule. Time dependent density functional theory calculations, using the LDA, BLYP, B3LYP, and SAOP functionals have been carried out for CuAg and the accuracy of TD-DFT has been compared with ab initio results.

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

Modeling Liquid Water by Climbing up Jacob’s Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials

Within the framework of Kohn–Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob’s ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric–isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Block-diagonalization as a tool for the robust diabatization of high-dimensional potential energy surfaces

Robust diabatization techniques are key for the development of high-dimensional coupled potential energy surfaces (PESs) to be used in multi-state quantum dynamics simulations. In the present study we demonstrate that, besides the actual diabatization technique, common problems with the underlying electronic structure calculations can be the reason why a diabatization fails. After giving a short review of the theoretical background of diabatization, we propose a method based on the block-diagonalization to analyse the electronic structure data. This analysis tool can be used in three different ways: First, it allows to detect issues with the ab initio reference data and is used to optimize the setup of the electronic structure calculations. Second, the data from the block-diagonalization are utilized for the development of optimal parametrized diabatic model matrices by identifying the most significant couplings. Third, the block-diagonalization data are used to fit the parameters of the diabatic model, which yields an optimal initial guess for the non-linear fitting required by standard or more advanced energy based diabatization methods. The new approach is demonstrated by the diabatization of 9 electronic states of the propargyl radical, yielding fully coupled full-dimensional (12D) PESs in closed form.

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

Ab initio benchmarks of neutrinoless double- β decay in light nuclei with a chiral Hamiltonian

Here, we report ab initio benchmark calculations of nuclear matrix elements (NMEs) for neutrinoless double-β (0νββ) decays in light nuclei with mass numbers ranging from A = 6 to A = 22. We use the transition operator derived from light-Majorana neutrino exchange and evaluate the NME with three different methods: two variants of in-medium similarity renormalization group (IMSRG) and importance-truncated no-core shell model (IT-NCSM). The same two plus three nucleon interaction from chiral effective field theory is employed, and both isospin-conserving (ΔT = 0) and isospin-changing (ΔT = 2) transitions are studied. We compare our resulting ground-state energies and NMEs to those of recent ab initio no-core shell model and coupled-cluster calculations, also with the same inputs. We show that the NMEs of ΔT = 0 transitions are in good agreement among all calculations, at the level of 10%. For ΔT = 2, relative deviations are more significant in some nuclei. The comparison with the exact IT-NCSM result allows us to analyze these cases in detail, and indicates the next steps toward improving the IMSRG-based approaches. The present study clearly demonstrates the power of consistent cross checks that are made possible by ab initio methodology. This capability is crucial for providing meaningful many-body uncertainties in the NMEs for the 0νββ decays in heavier candidate nuclei, where quasiexact benchmarks are not available.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Ab Initio Study of Electronic and Magnetic Properties of Germanene with Different Nonmagnetic Metal Adatoms

Electronic and magnetic properties of two-dimensional (2D) germanene (Ge) with five different adatoms have been analyzed and discussed by the DFT method. Different nonmagnetic metals adsorbed at different sites, on one hand, a magnetic moment is induced by Mg adatom in the germanene. On the other hand, the adsorptions of Al, Ga, Li, and Na show no magnetism. We further study the effect of strain on the magnetism in Mg-adsorbed germanene; we apply an isotropic tensile and compressive strain on the system. On the basis of our calculations, a tunable magnetism shows as the strain increases. The analysis of the PDOS shows that the s–p hybridization between Mg and Ge atoms results in such magnetic behavior. These magneticadsorbed germanene materials might show potential applications in the nanoscale devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Experimental and ab initio studies on sub-lattice ordering and magnetism in Co{sub 2}Fe(Ge{sub 1−x}Si{sub x}) alloys

Crystallographic and magnetic properties of bulk Co{sub 2}Fe(Ge{sub 1−x}Si{sub x}) alloys with 0 ≤ x ≤ 1, synthesized by arc melting method, have been studied. Co{sub 2}FeSi alloy has been found to crystallize with L2{sub 1} structure, but the super-lattice peaks are absent in the X-ray diffraction patterns of alloys containing high Ge concentration. Unit cell volume of this series of alloys decreased from 185.2 to 178.5 Å{sup 3} as Si content was increased from 0 to 1.00. All alloy compositions exhibit ferromagnetic behavior with a high Curie temperature (T{sub C}). T{sub C} showed a systematic variation with x. A comparison between the values of saturation magnetization (M{sub s}) and effective moment per magnetic atom p{sub c} estimated from the temperature dependent susceptibility data above T{sub C}, shows that the alloys have half-metallic character. The alloy with x = 0 follows Slater-Pauling (S-P) rule with M{sub s} of 5.99μ{sub B}. However, M{sub s} for the alloy with x = 1.00 was found to be 5.42μ{sub B}, which is lower than the value of 6.0μ{sub B} predicted by S-P rule. Since atomic disorder is known to affect the M{sub s} and electronic structure of these alloys, ab initio calculations were carried out to explain the deviation in observed M{sub s} from S-P rule prediction and the half-metallic character of the alloys. Ab initio calculations reveal that alloys with L2{sub 1} structure have M{sub s} value as predicted by S-P rule. However, introduction of 12.5% DO{sub 3} disorder, which occurs due to swapping of Co and Fe atoms in the unit cell, decreases M{sub s} of alloys with x > 0 from the S-P prediction to values obtained experimentally. The results analyzed from the view point of electronic structure of the alloys in different ordered states bring out the influence of disorder on the observed magnetic properties of these technologically important alloys.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Bi{sub 1−x}Nb{sub x}O{sub 1.5+x} (x=0.0625, 0.12) fast ion conductors: Structures, stability and oxide ion migration pathways

A combined experimental and computational study of Bi{sub 1−x}Nb{sub x}O{sub 1.5+x} (x=0.0625 and 0.12) has been carried out using laboratory X-ray, neutron and electron diffraction, impedance measurements and ab-initio molecular dynamics. We demonstrate that Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625}, previously reported to adopt a cubic fluorite-type superstructure, can form two different polymorphs depending on the synthetic method: a metastable cubic phase is produced by quenching; while slower cooling yields a stable material with a tetragonal √2×√2×1 superstructure, which undergoes a reversible phase transition into the cubic form at ~680 °C on subsequent reheating. Neutron diffraction reveals that the tetragonal superstructure arises mainly from ordering in the oxygen sublattice, with Bi and Nb remaining disordered, although structured diffuse scattering observed in the electron diffraction patterns suggests a degree of short-range ordering. Both materials are oxide ion conductors. On thermal cycling, Bi{sub 0.88}Nb{sub 0.12}O{sub 1.62} exhibits a decrease in conductivity of approximately an order of magnitude due to partial transformation into the tetragonal phase, but still exhibits conductivity comparable to yttria-stabilised zirconia (YSZ). Ab-initio molecular dynamics simulations performed on Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} show that oxide ion diffusion occurs by O{sup 2−} jumps between edge- and corner-sharing OM{sub 4} groups (M=Bi, Nb) via tetrahedral □M{sub 4} and octahedral □M{sub 6} vacancies. - Graphical abstract: Oxide ion migration in tetragonal Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} occurs by O{sup 2−} jumps between edge- and corner-sharing OM{sub 4} groups (M=Bi, Nb) via tetrahedral M{sub 4} and octahedral M{sub 6} vacancies. - Highlights: • Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} adopts a tetragonal √2×√2×1 fluorite superstructure. • Superstructure is due to ordering in the O-sublattice, with Bi/Nb disordered. • Bi{sub 0.9375}Nb{sub 0.0625}O{sub 1.5625} is a good oxide ion conductor. • O{sup 2−} jump between OM{sub 4} groups (M=Bi, Nb) via tetrahedral and octahedral vacancies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗
DOE OSTI2017

Quantum Many-Body Effects in Defective Transition-Metal-Oxide Superlattices

Strong electronic correlations, interfaces, and defects, and disorder each individually challenge the theoretical methods for predictions of materials properties. These challenges are all simultaneously present in complex transition-metal-oxide interfaces and superlattices, which are known to exhibit unique and unusual properties caused by multiple coupled degrees of freedom and strong electronic correlations. Here we show that ab initio quantum Monte Carlo (QMC) solutions of the many-electron problem are now possible for the full complexity of these systems. Within a single nonempirical theoretical approach, we unambiguously establish the site-specific stability of oxygen vacancies in the (LaFeO 3 ) 2 /(SrFeO 3 ) superlattice, accounting for experimental data, and predict their migration pathways. Further, QMC calculations are now capable of playing a major role in the elucidation of many-body phenomena in complex oxides previously out of reach of first-principles theories.

Approximation↗
DOE OSTI2018

Relative energies and electronic structures of CoO polymorphs through ab initio diffusion quantum Monte Carlo

Here, we present a many-body diffusion quantum Monte Carlo (DMC) study on the ground- and excited state properties of crystalline CoO polymorphs. To our knowledge, DMC is the only electronic structure method available to provide correct energetic ordering within experimental error bars between the three CoO polymorphs: rocksalt, wurtzite, and zinc blende. We compare these results to density functional theory (DFT) using state-of-the-art functionals such as SCAN. For the structural properties, such as the lattice parameters and bulk moduli, our results are comparable to HSE and SCAN. Using DMC, we calculated the indirect and direct optical gaps as 3.8(2) and 5.2(2) eV. Our indirect optical gap compares well with the conductivity measurements of 3.6(5) eV and GW calculations with 3.4 eV. Similarly, we obtained the DMC indirect and direct quasiparticle gaps as 3.9(2) and 5.5(2) eV. DMC direct quasiparticle gaps compare well with the direct band gap of 5.53 eV obtained from ellipsometry studies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Ab initio construction of magnetic phase diagrams in alloys: The case of Fe 1-x Mn x Pt

A first-principles approach to the construction of concentration-temperature magnetic phase diagrams of metallic alloys is presented. The method employs self-consistent total energy calculations based on the coherent potential approximation for partially ordered and noncollinear magnetic states and is able to account for competing interactions and multiple magnetic phases. The application to the Fe 1–x Mn x Pt “magnetic chameleon” system yields the sequence of magnetic phases at T = 0 and the c-T magnetic phase diagram in good agreement with experiment, and a new low-temperature phase is predicted at the Mn-rich end. The importance of non-Heisenberg interactions for the description of the magnetic phase diagram is demonstrated.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Mechanically Assisted Self‐Healing of Ultrathin Gold Nanowires

Abstract As the critical feature sizes of integrated circuits approaching sub‐10 nm, ultrathin gold nanowires (diameter <10 nm) have emerged as one of the most promising candidates for next‐generation interconnects in nanoelectronics. Also due to their ultrasmall dimensions, however, the structures and morphologies of ultrathin gold nanowires are more prone to be damaged during practical services, for example, Rayleigh instability can significantly alter their morphologies upon Joule heating, hindering their applications as interconnects. Here, it is shown that upon mechanical perturbations, predamaged, nonuniform ultrathin gold nanowires can quickly recover into uniform diameters and restore their smooth surfaces, via a simple mechanically assisted self‐healing process. By examining the local self‐healing process through in situ high‐resolution transmission electron microscopy, the underlying mechanism is believed to be associated with surface atomic diffusion as evidenced by molecular dynamics simulations. In addition, mechanical manipulation can assist the atoms to overcome the diffusion barriers, as suggested by ab initio calculations, to activate more surface adatoms to diffuse and consequently speed up the self‐healing process. This result can provide a facile method to repair ultrathin metallic nanowires directly in functional devices, and quickly restore their microstructures and morphologies by simple global mechanical perturbations.

Wang, Binjun↗