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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 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Crystal structures of human procathepsin H

Cathepsin H is a member of the papain superfamily of lysosomal cysteine proteases. It is the only known aminopeptidase in the family and is reported to be involved in cancer and other major diseases. Like many other proteases, it is synthesized as an inactive proenzyme. Although the crystal structure of mature porcine cathepsin H revealed the binding of the mini-chain and provided structural basis for the aminopeptidase activity, detailed structural and functional information on the inhibition and activation of procathepsin H has been elusive. Here we present the crystal structures of human procathepsin H at 2.00 Å and 1.66 Å resolution. These structures allow us to explore in detail the molecular basis for the inhibition of the mature domain by the prodomain. Comparison with cathepsin H structure reveals how mini-chain reorients upon activation. We further demonstrate that procathepsin H is not auto-activated but can be trans-activated by cathepsin L.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Ab initio study of nitrogen-multisubstituted neutral and positively charged C{sub 20} fullerene

Ab initio investigation of structural and electronic properties of Nitrogen doped fullerenes, obtained from C{sub 20} by replacing up to 10 C atoms with N atoms, are studied by means of first principals density functional theory calculations using numerical orbitals as basis sets. We have obtained the ground state structures for C{sub 20−n}N{sub n} for n=1-10. While substituting nitrogen atoms, we cannot substitute more than 9 nitrogen atoms. Nitrogen doping in C20 shows a significant change in density of states. For a better comparison with experimental measurements, we have also considered some positively charged ions and report the differences between properties of these ions and the corresponding neutral molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Towards a self-consistent analysis of the anisotropic galaxy two- and three-point correlation functions on large scales: application to mock galaxy catalogues

We establish a practical method for the joint analysis of anisotropic galaxy two- and three-point correlation functions (2PCF and 3PCF, respectively) on the basis of the decomposition formalism of the 3PCF using tripolar spherical harmonics. We perform such an analysis with MultiDark-Patchy mock catalogues to demonstrate and understand the benefit of the anisotropic 3PCF. We focus on scales above $80\, h^{-1}\, {\rm Mpc}$, and use information from the shape and the baryon acoustic oscillation (BAO) signals of the 2PCF and 3PCF. We also apply density field reconstruction to increase the signal-to-noise ratio of BAO in the 2PCF measurement, but not in the 3PCF measurement. In particular, we study in detail the constraints on the angular diameter distance and the Hubble parameter. We build a model of the bispectrum or 3PCF that includes the non-linear damping of the BAO signal in redshift space. We carefully account for various uncertainties in our analysis including theoretical models of the 3PCF, window function corrections, biases in estimated parameters from the fiducial values, the number of mock realizations to estimate the covariance matrix, and bin size. The joint analysis of the 2PCF and 3PCF monopole and quadrupole components shows a $30{{\ \rm per\ cent}}$ and $20{{\ \rm per\ cent}}$ improvement in Hubble parameter constraints before and after reconstruction of the 2PCF measurements, respectively, compared to the 2PCF analysis alone. Furthermore, this study clearly shows that the anisotropic 3PCF increases cosmological information from galaxy surveys and encourages further development of the modelling of the 3PCF on smaller scales than we consider.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Materials Data on BaSi(HO2)2 by Materials Project

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

36 MATERIALS SCIENCE↗
DOE OSTI2015

Investigation of Compton profiles of molecular methane and ethane

The Compton profiles of methane and ethane molecules have been determined at an incident photon energy of 20 keV based on the third generation synchrotron radiation, and the statistical accuracy of 0.2% is achieved near p{sub z} = 0. The density functional theory with aug-cc-pVTZ basis set was used to calculate the Compton profiles of methane and ethane. The present experimental Compton profiles are in better agreement with the theoretical calculations in the whole p{sub z} region than the previous experimental results, which indicates that the present experimental Compton profiles are accurate enough to serve as the benchmark data for methane and ethane molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Continual–quantum plasmonics with kinematical functions: dipolar resonance and nonlocal polarizability of simple metal made nanoparticles

In this work we formulate the theory of a mesoscopic oscillator equivalent to sp-electron excitations in simple metal made nanoparticles illuminated by incident light. The principles of continuum mechanics have been applied to maintain this goal: the primary hypotheses about the dependences of electron density function upon kinematical generalized coordinates, the stationary action principle, and the perturbation method. On their grounds, dynamic equations describing the motion of electron gas subject to alternating potentials together with the ground state equations have been derived. A methodological advantage of the latter is in the correct (qualitative and quantitative) prediction of Friedel oscillations and electron spill-out through an ion lattice with no demands to use high power computer resources as opposed to the orbital density functional theory. The dynamic equations allow studying of the nanoparticle resonant properties in an analytical form without need of numerically solving them. It has been shown with their use that the resonant frequency of the main dipolar resonance becomes the density functional of the ground state. On the basis of the dynamic equations, the theory of nonlocal polarizability has been deduced that does not impose the homogeneity (or weak inhomogeneity) constraints on the electron gas density. In this context the two following results are of importance. We manage to: (1) to demonstrate the effect of giant nonlocality of the dipole moment—its formation by the events separated by distances significantly larger than nanoparticle dimensions and temporal intervals much larger than the mean free time; (2) to derive the expression of the volumetric mode of compression-tension that is resonant on frequency of the main dipolar resonance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Effect of complex configurations on the description of properties of {sup 132}Sn beta decay

Gamow–Teller transitions in the beta decay of the {sup 132}Sn neutron-rich nucleus was described microscopically. The coupling of one- and two-phonon components of the wave functions was taken into account on the basis of Skyrme interactions featuring various contributions of the tensor component. A separable approximation of the particle—hole interaction made it possible tohole interaction perform calculations in a large configuration space. It was shown that an increase in the strength of the neutron—proton tensor interaction led to an increase in the energy of Gamow—Teller transitions. In addition, a decrease in the {sup 132}Sn half-life with respect to beta decay was obtained.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Simulated field-modulated x-ray absorption in titania

Here, we present a method to compute the x-ray absorption near-edge structure (XANES) spectra of solid-state transition metal oxides using real-time time-dependent density functional theory, including spin–orbit coupling effects. This was performed on bulk-mimicking anatase titania (TiO 2 ) clusters, which allows for the use of hybrid functionals and atom-centered all electron basis sets. Furthermore, this method was employed to calculate the shifts in the XANES spectra of the Ti L-edge in the presence of applied electric fields to understand how external fields can modify the electronic structure, and how this can be probed using x-ray absorption spectroscopy. Specifically, the onset of t 2g peaks in the Ti L-edge was observed to red shift and the e g peaks were observed to blue shift with increasing fields, attributed to changes in the hybridization of the conduction band (3d) orbitals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Specific Reaction Parameter Density Functional Based on the Meta-Generalized Gradient Approximation: Application to H 2 + Cu(111) and H 2 + Ag(111)

Specific reaction parameter density functionals (SRP-DFs), which can describe dissociative chemisorption reactions on metals to within chemical accuracy, have so far been based on exchange functionals within the generalized gradient approximation (GGA) and on GGA correlation functionals or van der Waals correlation functionals. These functionals are capable of describing the molecule–metal surface interaction accurately, but they suffer from the general GGA problem that this can be done only at the cost of a rather poor description of the metal. Here, we show that it is possible also to construct SRP-DFs for H 2 dissociation on Cu(111) based on meta-GGA functionals, introducing three new functionals based on the “made-simple” (MS) concept. The exchange parts of the three functionals (MS-PBEl, MS-B86bl, and MS-RPBEl) are based on the expressions for the PBE, B86b, and RPBE exchange functionals. Quasi-classical trajectory (QCT) calculations performed with potential energy surfaces (PESs) obtained with the three MS functionals reproduce molecular beam experiments on H 2 , D 2 + Cu(111) with chemical accuracy. Therefore, these three non-empirical functionals themselves are also capable of describing H2 dissociation on Cu(111) with chemical accuracy. Similarly, QCT calculations performed on the MS-PBEl and MS-B86bl PESs reproduced molecular beam and associative desorption experiments on D 2 , H 2 + Ag(111) more accurately than was possible with the SRP48 density functional for H 2 + Cu(111). Also, the three new MS functionals describe the Cu, Ag, Au, and Pt metals more accurately than the all-purpose Perdew–Burke–Ernzerhof (PBE) functional. The only disadvantage we noted of the new MS functionals is that, as found for the example of H 2 + Cu(111), the reaction barrier height obtained by taking weighted averages of the MS-PBEl and MS-RPBEl functionals is tunable over a smaller range (9 kJ/mol) than possible with the standard GGA PBE and RPBE functionals (33 kJ/mol). As a result of this restricted tunability, it is not possible to construct an SRP-DF for H 2 + Ag(111) on the basis of the three examined MS meta-GGA functionals.

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

Investigation of the pressure dependent thermodynamic and elastic properties of 1,3,5-triamino-2,4,6-trinitrobenzene using dispersion corrected density functional theory

The influence of pressure on the thermodynamic, structural, and elastic properties of the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecular crystal at T = 0 is systematically studied. Calculations are carried out using density functional theory methods in a plane wave basis set with dispersion corrections for the exchange-correlation part of total energy, and ultrasoft pseudopotentials. The equilibrium unit cell parameters, the cold compression curve in the pressure range of 0–50 GPa and the sound speeds are computed. The effect of finite pressure on the molecular structure of TATB is elucidated from the analysis of relative changes in the intra- and intermolecular geometrical parameters. For the first time, the full set of elastic constants of this crystal at zero and non-zero pressures is determined from ab initio calculations. The resulted structural, elastic, and acoustic properties of TATB are shown to be in a good agreement with available experimental and theoretical data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Long-term performance of engineered barriers for high-level waste repositories - 15358

The evolution of the engineered barrier system (EBS) of geological repositories for high-level radioactive waste (HLW) and spent fuel (SF) has been the subject of many national and international research programs during recent years. The emphasis of the research activities was on the elaboration of a detailed understanding of the complex coupled thermo-hydro-mechanical and -chemical (THM-C) processes, which are expected to evolve in the early post-closure period in the near field. From the perspective of radiological long-term safety, an in-depth understanding of these coupled processes is of great significance, because the evolution of the EBS during the early post-closure phase may have a non-negligible impact on the safety functions at later stages of the repository's lifetime. Process interactions during the re-saturation phase (heat pulse, gas generation, non-uniform water uptake from the host rock) could impair the homogeneity of the safety-relevant properties in the EBS (e.g. swelling pressure, hydraulic conductivity, diffusivity). The 7. Framework EURATOM PEBS project (long-term Performance of Engineered Barrier Systems) was initiated in 2010 and completed in March 2014. The project aimed at evaluating the sealing and barrier performance of clay-based EBS over time. The project approach included experiments, model development and consideration of the potential impact on long-term safety functions. The specific project aims were to: -deepen the understanding of the THM and THM-C evolution of the EBS system with time, - provide an enhanced quantitative basis for relating the evolutionary behavior to the safety functions, - clarify further the significance of residual uncertainties for long-term performance assessment. It can be concluded that uncertainties in process understanding occurring in the re-saturation period have been better constrained through PEBS studies, thus the uncertainties in the long-term performance of bentonite barriers have been reduced in some areas. Improvements are in the areas of evolution of materials properties and model development and testing at various scales. On-going in-situ experiments in underground research laboratories may play an important role in further confirming bentonite performance over periods of 10 - 20 years. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2011

Efficiently enclosing the compact binary parameter space by singular-value decomposition

Gravitational-wave searches for the merger of compact binaries use matched filtering as the method of detecting signals and estimating parameters. Such searches construct a fine mesh of filters covering a signal parameter space at high density. Previously it has been shown that singular-value decomposition can reduce the effective number of filters required to search the data. Here we study how the basis provided by the singular-value decomposition changes dimension as a function of template-bank density. We will demonstrate that it is sufficient to use the basis provided by the singular-value decomposition of a low-density bank to accurately reconstruct arbitrary points within the boundaries of the template bank. Since this technique is purely numerical, it may have applications to interpolating the space of numerical relativity waveforms.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Development and transferability of neural-network models for plasma-surface interactions

Plasma-surface interactions are increasingly critical to modern technologies; yet, accurate molecular dynamics simulations remain limited by the capabilities of interatomic potentials. Deep Potentials (DPs) promise to revolutionize the field by providing a systematic method for producing accurate interatomic potentials. The primary challenge of DP development is selecting a dataset, which efficiently spans the set of atomic environments one expects to encounter in the subsequent molecular dynamics simulations. The computational cost of density functional theory calculations, which are the typical basis for DP development, makes it impossible to directly verify the quality of a given DP. To address this challenge, we explore the development of a deep-learned interatomic potential, “DeepREBO,” trained to reproduce the behavior of the REBO2 empirical potential, enabling direct validation of training methodology and transferability. Using an active learning framework, we begin with a minimal dataset and iteratively expand it to train a Deep Potential-Smooth Edition model that faithfully reproduces REBO2 results for 25 eV hydrogen bombardment of diamond (001), a particularly challenging case. We show that small, carefully curated datasets can outperform large, unguided ones, with effective models requiring fewer than 15 000 snapshots. Subsequent transferability tests demonstrate that while DeepREBO generalizes well to diamond (111) surfaces, performance degrades for amorphous carbon or higher-energy impacts, highlighting the need for use-case-specific training data. We also evaluate methods to improve short-range repulsion. This study outlines best practices for training robust deep potentials and underscores the importance of dataset design for predictive plasma simulations.

Ab-initio molecular dynamics↗
DOE OSTI2016

Communication: Toward an improved control of the fixed-node error in quantum Monte Carlo: The case of the water molecule

All-electron Fixed-node Diffusion Monte Carlo calculations for the nonrelativistic ground-state energy of the water molecule at equilibrium geometry are presented. The determinantal part of the trial wavefunction is obtained from a selected Configuration Interaction calculation [Configuration Interaction using a Perturbative Selection done Iteratively (CIPSI) method] including up to about 1.4 × 10{sup 6} of determinants. Calculations are made using the cc-pCVnZ family of basis sets, with n = 2 to 5. In contrast with most quantum Monte Carlo works no re-optimization of the determinantal part in presence of a Jastrow is performed. For the largest cc-pCV5Z basis set the lowest upper bound for the ground-state energy reported so far of −76.437 44(18) is obtained. The fixed-node energy is found to decrease regularly as a function of the cardinal number n and the Complete Basis Set limit associated with exact nodes is easily extracted. The resulting energy of −76.438 94(12) — in perfect agreement with the best experimentally derived value — is the most accurate theoretical estimate reported so far. We emphasize that employing selected configuration interaction nodes of increasing quality in a given family of basis sets may represent a simple, deterministic, reproducible, and systematic way of controlling the fixed-node error in diffusion Monte Carlo.

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

GDB-9-Ex_TD-DFT-PBE0: Dataset containing Time Dependent Density Functional Theory (TDDFT) calculations for organic molecules of the GDB-9-Ex dataset.

This dataset contains data-intensive quantum chemical electronic structure calculations for 96,766 organic molecules of the GDB-9-Ex dataset. Calculations were performed using the Time Dependent Density Functional Theory (TDDFT) first principles method using the ORCA software. It provides UV-vis spectra calculations of molecules with a high level of accuracy. The optical spectra behavior was collected based on the optimized molecular geometries in the DFTB method with 3ob parameters. All calculations utilized the def2-TZVP basis sets with the auxiliary def2/J and def2-TZVP/C basis sets. The time-dependent density-functional theory (TDDFT) approach with the PBE0 exchange-correlation functional and ORCAs default integration grid was employed. For the excitation energy calculations, the lowest 50 excitation states were calculated.

AI dataset↗
DOE OSTI2013

Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: Theory, implementation, and examples

Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H{sup -}, and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, {theta}. Standard basis sets that are optimized for not-complex-scaled calculations ({theta} = 0) are not sufficiently flexible to describe the {theta}-dependence of the wave functions even when heavily augmented by additional sets.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

On the combined experimental and theoretical investigations on 3-nitrophenylamine for nonlinear optical applications

Single crystal of 3-Nitrophenylamine (3-NPA) was grown using methanol as solvent by slow evaporation technique. The cell parameters and crystal structure was elucidated by single crystal X-ray diffraction analysis. The laser damage threshold of the title compound was measured using Nd:YAG laser. The second harmonic generation (SHG) nonlinearity was measured using Kurtz-Perry powder technique. The optimized geometry, dipole moment, polarizability and first order hyperpolarizability were obtained by density functional theory (DFT) using 6-31++G (d, p) basis set.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si$_2$H$_6$ which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗