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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Approximating Density Probability Distribution Functions Across Cosmologies

Using a suite of self-similar cosmological simulations, we measure the probability distribution functions (PDFs) of real-space density, redshift-space density, and their geometric mean. We find that the real-space density PDF is well-described by a function of two parameters: ns, the spectral slope, and σL, the linear rms density fluctuation. For redshift-space density and the geometric mean of real- and redshift-space densities, we introduce a third parameter, ${s}_{L}=\sqrt{\langle {\left({{dv}}_{\mathrm{pec}}^{L}/{dr}\right)}^{2}\rangle }/H$. We find that density PDFs for the LCDM cosmology is also well-parameterized by these three parameters. As a result, we are able to use a suite of self-similar cosmological simulations to approximate density PDFs for a range of cosmologies. We make the density PDFs publicly available and provide an analytical fitting formula for them.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Non-adiabatic approximations in time-dependent density functional theory: progress and prospects

Time-dependent density functional theory continues to draw a large number of users in a wide range of fields exploring myriad applications involving electronic spectra and dynamics. Although in principle exact, the predictivity of the calculations is limited by the available approximations for the exchange-correlation functional. In particular, it is known that the exact exchange-correlation functional has memory-dependence, but in practise adiabatic approximations are used which ignore this. Here we review the development of non-adiabatic functional approximations, their impact on calculations, and challenges in developing practical and accurate memory-dependent functionals for general purposes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Calculation and interpretation of classical turning surfaces in solids

Abstract Classical turning surfaces of Kohn–Sham potentials separate classically allowed regions (CARs) from classically forbidden regions (CFRs). They are useful for understanding many chemical properties of molecules but need not exist in solids, where the density never decays to zero. At equilibrium geometries, we find that CFRs are absent in perfect metals, rare in covalent semiconductors at equilibrium, but common in ionic and molecular crystals. In all materials, CFRs appear or grow as the internuclear distances are uniformly expanded. They can also appear at a monovacancy in a metal. Calculations with several approximate density functionals and codes confirm these behaviors. A classical picture of conduction suggests that CARs should be connected in metals, and disconnected in wide-gap insulators, and is confirmed in the limits of extreme compression and expansion. Surprisingly, many semiconductors have no CFR at equilibrium, a key finding for density functional construction. Nonetheless, a strong correlation with insulating behavior can still be inferred. Moreover, equilibrium bond lengths for all cases can be estimated from the bond type and the sum of the classical turning radii of the free atoms or ions.

Chemistry↗
DOE OSTI2015

First-principle natural band alignment of GaN / dilute-As GaNAs alloy

Density functional theory (DFT) calculations with the local density approximation (LDA) functional are employed to investigate the band alignment of dilute-As GaNAs alloys with respect to the GaN alloy. Conduction and valence band positions of dilute-As GaNAs alloy with respect to the GaN alloy on an absolute energy scale are determined from the combination of bulk and surface DFT calculations. The resulting GaN / GaNAs conduction to valence band offset ratio is found as approximately 5:95. Our theoretical finding is in good agreement with experimental observation, indicating the upward movements of valence band at low-As content dilute-As GaNAs are mainly responsible for the drastic reduction of the GaN energy band gap. In addition, type-I band alignment of GaN / GaNAs is suggested as a reasonable approach for future device implementation with dilute-As GaNAs quantum well, and possible type-II quantum well active region can be formed by using InGaN / dilute-As GaNAs heterostructure.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Identifying attributes of CO 2 leakage zones in shallow aquifers using a parametric level set method: Original Research Article: Identifying attributes of CO 2 leakage zones in shallow aquifers using a parametric level set method

Leakage through abandoned wells and geologic faults poses the greatest risk to CO 2 storage permanence. For shallow aquifers, secondary CO 2 plumes emanating from the leak zones may go undetected for a sustained period of time and has the greatest potential to cause large-scale and long-term environmental impacts. Identification of the attributes of leak zones, including their shape, location, and strength, is required for environmental risk assessment. This study applies a parametric level set (PaLS) method to characterize leak zones. Level set methods are appealing for tracking topological changes and recovering unknown shapes of objects. However, level set evolution using the conventional level set methods is computationally challenging. In PaLS, the level set function is approximated by using a weighted sum of basis functions and the level set evolution problem is replaced by an optimization problem. The efficacy of PaLS is demonstrated by reconstructing attributes of a CO 2 leak zone in a carbonate aquifer. Our results show that PaLS is a robust source identification method that can recover the approximate leak zone locations in the presence of measurement errors, model parameter uncertainty, and inaccurate guesses of source flux strengths. Accurate delineation of source geometry is achievable when a relatively dense observation network is used. The PaLS-based, source recovery framework introduced in this work is generic and can be adapted for any reactive transport model by simply switching the pre- and post-processing routines.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Fast approximation to supershell partition functions: Explicit forms of the coefficients

In a previous work, we derived a formula for supershell partition functions, which are the cornerstone of the Super-Transition-Array approach to radiative-opacity calculations. The new expression takes the form of a functional of the distribution of energies within the supershell and allows for fast and accurate computations, truncating the number of terms in the expansion. The latter involves coefficients (denoted Γ $k$ ) for which we obtained a recursion relation. In the present short paper, as a complement of the previous one, we give an explicit formula for the coefficients Γ $k$ . Another recursion relation is also provided, as well as an alternative expression involving Bell polynomials. In conclusion, the connections with cycle indexes of permutation groups and with elementary symmetric polynomials are outlined.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Applicability of the thin-film approximation in terahertz photoconductivity measurements

Thin mesoporous photoconductive layers are critically important for efficient water-spitting solar cells. A detailed understanding of photoconductivity in these materials can be achieved via terahertz transient absorption measurements. Such measurements are commonly interpreted using the thin-film approximation. We compare this approximation with a numerical solution of the transfer function without approximations using experimental results for thin-film mesoporous tin oxide (SnO 2 ) samples which range in thickness from 3.3 to 12.6 µm. These samples were sensitized with either a ruthenium polypyridyl complex or a porphyrin dye. The two sensitizers have markedly different absorption coefficients, resulting in penetration depths of 15 µm and 1 µm, respectively. The thin-film approximation results are in good agreement with the numerical work-up for the short penetration length dye. For the longer penetration length samples, the thin-film formula fails even for thicknesses of only 3 µm ≈ λ/100. The imaginary part of the conductivity calculated using the thin-film formula was significantly larger in magnitude than the value without approximations. This discrepancy between the commonly used thin-film approximation and the numerical solution demonstrates the need for a careful analysis of the thin-film formula.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Assessment of exchange-correlation functionals on oxygen vacancy formation energies of metal oxides

Oxygen vacancies are a common defect in oxides and play vital roles in many technological applications such as oxygen separation, catalytic reactors, solid oxide fuel cells, and solar thermochemical water splitting. The oxygen vacancy formation energy is directly related to the oxide reduction enthalpy and the vacancy concentration and, therefore, is a key quantity underlying these applications. The complexity of measuring oxygen vacancy formation energies experimentally suggests the utility of calculations based on density functional theory (DFT). However, the calculated results are strongly dependent on the exchange-correlation functionals and other parameters such as the Hubbard U . In this work, we compare the performance of the meta-GGA strongly constrained and appropriately normed (SCAN) functional and the commonly used semilocal generalized gradient approximation (GGA) functionals with experimental values of structural parameters, band gaps, magnetic structures, and oxygen vacancy formation energies for six representative oxides, i.e., CaMnO 3 , SrMnO 3 , LaMnO 3 , YMnO 3 , LaFeO 3 , and CeO 2 . Further, our results show that SCAN usually has better agreement with the experimental lattice constants and band gaps and larger magnetic moments than the commonly used GGA functionals. Although SCAN overestimates the oxygen vacancy formation energies of transition metal oxides and therefore requires unusually large Hubbard U values to reproduce the experimental reduction enthalpies, it does predict the correct oxygen vacancy formation energy of CeO 2 , which challenges the commonly used GGA and hybrid functionals. Our results underscore the challenges that exist in describing these complex oxides by DFT and may shed light on developing more accurate exchange-correlation functionals for oxygen vacancy formation energy calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Natively Periodic Fast Multipole Method: Approximating the Optimal Green’s Function

The fast multipole method (FMM) obeys periodic boundary conditions "natively" if it uses a periodic Green's function for computing the multipole expansion in the interaction zone of each FMM oct-tree node. One can define the "optimal" Green's function for such a method that results in the numerical solution that converges to the equivalent particle-mesh (PM) solution in the limit of sufficiently high order of multipoles. A discrete functional equation for the optimal Green's function can be derived, but is not practically useful as methods for its solution are not known. Instead, this paper presents an approximation for the optimal Green's function that is accurate to better than 10 -3 in ${L}_{\mathrm{MAX}}$ norm and 10 -4 in L 2 norm for practically useful multipole counts. Such an approximately optimal Green's function offers a practical way for implementing the FMM with periodic boundary conditions natively, without the need to compute lattice sums or to rely on hybrid FMM-PM approaches.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Structural stability and defect energetics of ZnO from diffusion quantum Monte Carlo

We have applied the many-body ab initio diffusion quantum Monte Carlo (DMC) method to study Zn and ZnO crystals under pressure and the energetics of the oxygen vacancy, zinc interstitial, and hydrogen impurities in ZnO. We show that DMC is an accurate and practical method that can be used to characterize multiple properties of materials that are challenging for density functional theory (DFT) approximations. DMC agrees with experimental measurements to within 0.3 eV, including the band-gap of ZnO, the ionization potential of O and Zn, and the atomization energy of O{sub 2}, ZnO dimer, and wurtzite ZnO. DMC predicts the oxygen vacancy as a deep donor with a formation energy of 5.0(2) eV under O-rich conditions and thermodynamic transition levels located between 1.8 and 2.5 eV from the valence band maximum. Our DMC results indicate that the concentration of zinc interstitial and hydrogen impurities in ZnO should be low under n-type and Zn- and H-rich conditions because these defects have formation energies above 1.4 eV under these conditions. Comparison of DMC and hybrid functionals shows that these DFT approximations can be parameterized to yield a general correct qualitative description of ZnO. However, the formation energy of defects in ZnO evaluated with DMC and hybrid functionals can differ by more than 0.5 eV.

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

Meshfree Methods

Meshfree methods have undergone substantial development and have received much attention in the last two decades. This new family of numerical methods is designed to inherit the main advantages of the finite element method such as compact supports of shape functions and good approximation properties while, at the same time, overcome the main disadvantages of the finite element method caused by the mesh dependence. The meshfree methods share a common feature that no mesh is needed and shape functions are constructed from sets of points, thus eliminating the need for time consuming mesh generation. The most significant advantage of meshfree methods is the flexibility in customizing approximation functions for desired regularity and for capturing essential physics and features of the particular problems of interest. Adaptivity formulation and multiple-scale solution strategies also can be implemented with relative ease. It has become clear that the meshfree methods provide considerable advantages over the conventional finite element methods in solving problems involving moving discontinuities, evolving material interfaces, multiple-scale phenomena, large material distortion and structural deformation, and fracture and damage processes. This Chapter gives an overview of many classes of meshfree methods, with more detailed discussions on Smoothed Particle Hydrodynamics (SPH), the Reproducing Kernel Particle Method (RKPM), Peridynamics (PD), the Material Point Method (MPM), as well as their applications in various challenging engineering problems.2

Chen, Jiun-Shyan↗
DOE OSTI2023

Benchmark Data Set of Crystalline Organic Semiconductors

This work reports a Benchmark Data set of Crystalline Organic Semiconductors to test calculations of the structural and electronic properties of these materials in the solid state. The data set contains 67 crystals consisting of mostly rigid molecules with a single dominant conformer, covering the majority of known structural types. The experimental crystal structure is available for the entire data set, whereas zero-temperature unit cell volume can be reliably estimated for a subset of 28 crystals. Using this subset, we benchmark r 2 SCAN-D3 and PBE-D3 density functionals. Then, for the entire data set, we benchmark approximate density functional theory (DFT) methods, including GFN1-xTB and DFTB3(3ob-3-1), with various dispersion corrections against r 2 SCAN-D3. Our results show that r 2 SCAN-D3 geometries are accurate within a few percent, which is comparable to the statistical uncertainty of experimental data at a fixed temperature, but the unit cell volume is systematically underestimated by 2% on average. The several times faster PBE-D3 provides an unbiased estimate of the volume for all systems except for molecules with highly polar bonds, for which the volume is substantially overestimated in correlation with the underestimation of atomic charges. Considered approximate DFT methods are orders of magnitude faster and provide qualitatively correct but overcompressed crystal structures unless the dispersion corrections are fitted by unit cell volume.

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

Thermally-assisted-occupation density functional theory with generalized-gradient approximations

We extend the recently proposed thermally-assisted-occupation density functional theory (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)] to generalized-gradient approximation (GGA) exchange-correlation density functionals. Relative to our previous TAO-LDA (i.e., the local density approximation to TAO-DFT), the resulting TAO-GGAs are significantly superior for a wide range of applications, such as thermochemistry, kinetics, and reaction energies. For noncovalent interactions, TAO-GGAs with empirical dispersion corrections are shown to yield excellent performance. Due to their computational efficiency for systems with strong static correlation effects, TAO-LDA and TAO-GGAs are applied to study the electronic properties (e.g., the singlet-triplet energy gaps, vertical ionization potentials, vertical electron affinities, fundamental gaps, and symmetrized von Neumann entropy) of acenes with different number of linearly fused benzene rings (up to 100), which is very challenging for conventional electronic structure methods. The ground states of acenes are shown to be singlets for all the chain lengths studied here. With the increase of acene length, the singlet-triplet energy gaps, vertical ionization potentials, and fundamental gaps decrease monotonically, while the vertical electron affinities and symmetrized von Neumann entropy (i.e., a measure of polyradical character) increase monotonically.

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

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.

Willow, Soohaeng Y.↗
DOE OSTI2019

The role of decomposition reactions in assessing first-principles predictions of solid stability

Abstract The performance of density functional theory approximations for predicting materials thermodynamics is typically assessed by comparing calculated and experimentally determined enthalpies of formation from elemental phases, Δ H f . However, a compound competes thermodynamically with both other compounds and their constituent elemental forms, and thus, the enthalpies of the decomposition reactions to these competing phases, Δ H d , determine thermodynamic stability. We evaluated the phase diagrams for 56,791 compounds to classify decomposition reactions into three types: 1. those that produce elemental phases, 2. those that produce compounds, and 3. those that produce both. This analysis shows that the decomposition into elemental forms is rarely the competing reaction that determines compound stability and that approximately two-thirds of decomposition reactions involve no elemental phases. Using experimentally reported formation enthalpies for 1012 solid compounds, we assess the accuracy of the generalized gradient approximation (GGA) (PBE) and meta-GGA (SCAN) density functionals for predicting compound stability. For 646 decomposition reactions that are not trivially the formation reaction, PBE (mean absolute difference between theory and experiment (MAD) = 70 meV/atom) and SCAN (MAD = 59 meV/atom) perform similarly, and commonly employed correction schemes using fitted elemental reference energies make only a negligible improvement (~2 meV/atom). Furthermore, for 231 reactions involving only compounds (Type 2), the agreement between SCAN, PBE, and experiment is within ~35 meV/atom and is thus comparable to the magnitude of experimental uncertainty.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗