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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Predicting a quaternary tungsten oxide for sustainable photovoltaic application by density functional theory

A quaternary oxide, CuSnW{sub 2}O{sub 8} (CTTO), has been predicted by density functional theory (DFT) to be a suitable material for sustainable photovoltaic applications. CTTO possesses band gaps of 1.25 eV (indirect) and 1.37 eV (direct), which were evaluated using the hybrid functional (HSE06) as a post-DFT method. The hole mobility of CTTO was higher than that of silicon. Further, optical absorption calculations demonstrate that CTTO is a better absorber of sunlight than Cu{sub 2}ZnSnS{sub 4} and CuIn{sub x}Ga{sub 1−x}Se{sub 2} (x = 0.5). In addition, CTTO exhibits rigorous thermodynamic stability comparable to WO{sub 3}, as investigated by different thermodynamic approaches such as bonding cohesion, fragmentation tendency, and chemical potential analysis. Chemical potential analysis further revealed that CTTO can be synthesized at flexible experimental growth conditions, although the co-existence of at least one secondary phase is likely. Finally, like other Cu-based compounds, the formation of Cu vacancies is highly probable, even at Cu-rich growth condition, which could introduce p-type activity in CTTO.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Construction of meta-GGA functionals through restoration of exact constraint adherence to regularized SCAN functionals

The strongly constrained and appropriately normed (SCAN) meta-GGA exchange–correlation functional is constructed as a chemical environment-determined interpolation between two separate energy densities: one describes single-orbital electron densities accurately and another describes slowly varying densities accurately. To conserve constraints known for the exact exchange–correlation functional, the derivatives of this interpolation vanish in the slowly varying limit. While theoretically convenient, this choice introduces numerical challenges that degrade the functional’s efficiency. We have recently reported a modification to the SCAN meta-GGA, termed restored-regularized-SCAN (r 2 SCAN) , that introduces two regularizations into SCAN, which improve its numerical performance at the expense of not recovering the fourth order term of the slowly varying density gradient expansion for exchange. Here, we show the derivation of a progression of density functional approximations [regularized SCAN (rSCAN), r++SCAN, r 2 SCAN, and r 4 SCAN] with increasing adherence to exact conditions while maintaining a smooth interpolation. The greater smoothness of r 2 SCAN seems to lead to better general accuracy than the additional exact constraint of SCAN or r 4 SCAN does.

, correlation energy↗
DOE OSTI2020

Functional equations and separation of variables for exact g -function

The g-function is a measure of degrees of freedom associated to a boundary of two-dimensional quantum field theories. In integrable theories, it can be computed exactly in a form of the Fredholm determinant, but it is often hard to evaluate numerically. In this paper, we derive functional equations — or equivalently integral equations of the thermodynamic Bethe ansatz (TBA) type — which directly compute the g-function in the simplest integrable theory; the sinh-Gordon theory at the self-dual point. The derivation is based on the classic result by Tracy and Widom on the relation between Fredholm determinants and TBA, which was used also in the context of topological string. We demonstrate the efficiency of our formulation through the numerical computation and compare the results in the UV limit with the Liouville CFT. As a side result, we present multiple integrals of Q-functions which we conjecture to describe a universal part of the g-function, and discuss its implication to integrable spin chains.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated under three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Accurate Binding Energies for Lithium Polysulfides and Assessment of Density Functionals for Lithium–Sulfur Battery Research

Lithium–sulfur batteries have high theoretical energy density, but a better knowledge of their intimate structural details will be helpful in improving their conductivity and long-term cycling behavior. In order to identify the stationary configurations of lithium polysulfides (Li 2 S n , 2 ≤ n ≤ 8) formed in the charging and discharging processes of the lithium–sulfur batteries, ab initio molecular dynamics was employed to sample the configuration space of Li 2 S n , followed by optimization of structures by CCSD(T)-F12b/aug-cc-pVDZ. Here, using the optimized stationary points, we have created the LiSAE38 benchmark database of atomization energies (AEs) of 38 lithium polysulfide isomers by using the higher-level WMS and W3X-L methods. In addition, the performances of 39 density functionals have been assessed against the benchmark AEs and the relative stabilities of Li 2 S n isomers. On the basis of the assessments with the def2-QZVP basis set, the PW6B95, B97-1, B3LYP-D3, TPSS, and DSD-PBEP86 density functionals are the most accurate for the AEs, whereas the mPW2-PLYP-D, DSD-PBEP86, PW6B95, HSE06, and PBEQIDH functionals are most accurate for the relative energies. Local functionals are of special interest because of their lower cost (faster timings in terms of computer resources) for large systems; among the tested local functionals, MN15-L and revM06-L are the most accurate for the calculations of relative stabilities.

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

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree–Fock and density functional theory via linear response

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using a numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2 , Be, N 2 , H 2 O, and C 2 H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

β-Functionalized trans -A2B2 push–pull tetrabenzoporphyrins

A series of β-functionalized trans-A2B2 tetrabenzoporphyrins have been successfully designed and synthesized through newly developed regioselective bromination chemistry of porphyrins and a Pd(0) catalyzed three-step-one pot reaction. These benzoporphyrins exhibit unique patterns of UV-Vis absorptions and emissions. Tetrabenzoporphyrins possess a unique combination of photophysical, optoelectronic, and physicochemical properties due to their largely extended π-conjugation and associated dynamics of ring deformation which make them distinctive from their parent porphyrins. As compared with their parent porphyrins, tetrabenzoporphyrins often display significantly red-shifted absorption bands, a much-desired feature for various applications ranging from biomedicine to organic electronics. However, due to limited synthetic methods, only a small number of simple symmetrical tetrabenzoporphyrins have been available for study. Unsymmetrical tetrabenzoporphyrins, in particular those functionalized at the porphyrin β-positions, are very difficult to access. A2B2 porphyrins, on the other hand, represent an attractive class of materials for non-linear optical applications as well as for other applications such as those involving dye-sensitized solar cells. meso-Functionalized push–pull trans-A2B2 porphyrins have previously been made available through the Suzuki coupling reaction, the Heck reaction and the Sonogashira coupling reaction of 5,10-dibromoporphyrin with the corresponding alkyl boronic acids, olefins and alkynes, respectively and have demonstrated interesting non-linear optical properties. In contrast, β-functionalized push–pull A2B2 porphyrins of the type shown in Fig. 1 have until now remained unknown. Furthermore, we present the synthesis and characterization for the first examples of β-functionalized A2B2 push–pull tetrabenzoporphyrins.

Kumar, Siddhartha↗
DOE OSTI2018

Low thyroid function is not associated with an accelerated deterioration in renal function

Abstract Background Chronic kidney disease (CKD) is frequently accompanied by thyroid hormone dysfunction. It is currently unclear whether these alterations are the cause or consequence of CKD. This study aimed at studying the effect of thyroid hormone alterations on renal function in cross-sectional and longitudinal analyses in individuals from all adult age groups. Methods Individual participant data (IPD) from 16 independent cohorts having measured thyroid stimulating hormone, free thyroxine levels and creatinine levels were included. Thyroid hormone status was defined using clinical cut-off values. Estimated glomerular filtration rates (eGFR) were calculated by means of the four-variable Modification of Diet in Renal Disease (MDRD) formula. For this IPD meta-analysis, eGFR at baseline and eGFR change during follow-up were computed by fitting linear regression models and linear mixed models in each cohort separately. Effect estimates were pooled using random effects models. Results A total of 72 856 individuals from 16 different cohorts were included. At baseline, individuals with overt hypothyroidism (n = 704) and subclinical hypothyroidism (n = 3356) had a average (95% confidence interval) −4.07 (−6.37 to −1.78) and −2.40 (−3.78 to −1.02) mL/min/1.73 m2 lower eGFR as compared with euthyroid subjects (n = 66 542). In (subclinical) hyperthyroid subjects (n = 2254), average eGFR was 3.01 (1.50–4.52) mL/min/1.73 m2 higher. During 329 713 patient years of follow-up, eGFR did not decline more rapidly in individuals with low thyroid function compared with individuals with normal thyroid function. Conclusions Low thyroid function is not associated with a deterioration of renal function. The cross-sectional association may be explained by renal dysfunction causing thyroid hormone alterations.

Meuwese, Christiaan L.↗
DOE OSTI2025

Source function from two-particle correlation function through entropy-regularized Richardson-Lucy deblurring

Source functions are obtained from p – p and d – α correlation functions by applying the Richardson-Lucy (RL) deblurring to the Koonin-Pratt (KP) equation. To prevent fitting of noise in the correlation function, total-variation (TV) regularization is employed that has been effective in ordinary image restoration. TV alone cannot ensure normalization of the source functions. To ensure the latter, we propose a maximum-entropy regularized RL algorithm (MEM-RL). We outline the MEM-RL formalism and optimization strategy for the KP equation, demonstrating its effectiveness on both simulated and experimental data, including the p – p and d – α correlation functions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

QuantImPy: Minkowski functionals and functions with Python

The Minkowski functionals and functions are a family of morphological measures and can be used to describe both the morphology (shape) and topology (connectedness) of a system. This paper presents the QuantImPy Python package which can compute both the Minkowski functionals and functions. In addition, this package can efficiently perform basic morphological operations and compute their distance maps. QuantImPy is easy to install, well documented, integrated with existing Python packages, and open source.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗