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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 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
NASA NTRS1990

Toward modeling a dynamic biological neural network

The organization of a mammalian macular endorgan is interpreted on physical and engineering principles. Having accomplished this task, it is possible to mathematically and symbolically model information processing by the macular neural network. A complex symbolic model is produced through use of mathematical notations that describe the functioning system. The model, consisting of six tiers, is constructed to mimic the neural system. On the basis of initial simulations, it is concluded that the network functions best when some of the detecting elements (i.e., type I hair cells) are weakly inhibitory. The simulations also illustrate the importance of disinhibition of receptors located in the third tier in shaping nerve discharge patterns at the sixth tier in the model system.

Ross, M. D.↗
DOE OSTI2011

Scattering in multilayered structures: Diffraction from a nanohole

The spectral expansion of the Green's tensor for a planar multilayered structure allows us to semianalytically obtain the angular spectrum representation of the field scattered by an arbitrary dielectric perturbation present in the structure. In this paper we present a method to find the expansion coefficients of the scattered field, given that the electric field inside the perturbation is available. The method uses a complete set of orthogonal vector wave functions to solve the structure's vector wave equation. In the two semi-infinite bottom and top media, those vector wave functions coincide with the plane-wave basis vectors, including both propagating and evanescent components. The technique is used to obtain the complete angular spectrum of the field scattered by a nanohole in a metallic film under Gaussian illumination. We also show how the obtained formalism can easily be extended to spherically and cylindrically multilayered media. In those cases, the expansion coefficients would multiply the spherical and cylindrical vector wave functions.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl Isomerases

Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure:function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1976

A kinetic-theory approach to turbulent chemically reacting flows

The paper examines the mathematical and physical foundations for the kinetic theory of reactive turbulent flows, discussing the differences and relation between the kinetic and averaged equations, and comparing some solutions of the kinetic equations obtained by the Green's function method with those obtained by the approximate bimodal method. The kinetic method described consists essentially in constructing the probability density functions of the chemical species on the basis of solutions of the Langevin stochastic equation for the influence of eddies on the behavior of fluid elements. When the kinetic equations are solved for the structure of the diffusion flame established in a shear layer by the bimodal method, discontinuities in gradients of the mean concentrations at the two flame edges appear. This is a consequence of the bimodal approximation of all distribution functions by two dissimilar half-Maxwellian functions, which is a very crude approximation. These discontinuities do not appear when the solutions are constructed by the Green's function method described here.

Chung, P. M.↗
NASA NTRS1988

MODIS information, data and control system (MIDACS) level 2 functional requirements

The MODIS Information, Data and Control System (MIDACS) Level 2 Functional Requirements Document establishes the functional requirements for MIDACS and provides a basis for the mutual understanding between the users and the designers of the EosDIS, including the requirements, operating environment, external interfaces, and development plan. In defining the requirements and scope of the system, this document describes how MIDACS will operate as an element of the EOS within the EosDIS environment. This version of the Level 2 Requirements Document follows an earlier release of a preliminary draft version. The sections on functional and performance requirements do not yet fully represent the requirements of the data system needed to achieve the scientific objectives of the MODIS instruments and science teams. Indeed, the team members have not yet been selected and the team has not yet been formed; however, it has been possible to identify many relevant requirements based on the present concept of EosDIS and through interviews and meetings with key members of the scientific community. These requirements have been grouped by functional component of the data system, and by function within each component. These requirements have been merged with the complete set of Level 1 and Level 2 context diagrams, data flow diagrams, and data dictionary.

Han, D.↗
DOE OSTI2015

On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH{sub 4}, NH{sub 3}, H{sub 2}O, SiH{sub 4}, PH{sub 3}, SH{sub 2}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and C{sub 2}H{sub 6}. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Importance of imposing gauge invariance in time-dependent density functional theory calculations with meta-generalized gradient approximations

It has been known for more than a decade that the gauge variance of the kinetic energy density τ leads to additional terms in the magnetic orbital rotation Hessian used in linear-response time-dependent density functional theory (TDDFT), affecting excitation energies obtained with τ-dependent exchange–correlation functionals. While previous investigations found that a correction scheme based on the paramagnetic current density has a small effect on benchmark results, we report more pronounced effects here, in particular, for the popular M06-2X functional and for some other meta-generalized gradient approximations (mGGAs). In the first part of this communication, this is shown by a reassessment of a set of five Ni(II) complexes for which a previous benchmark study that did not impose gauge invariance has found surprisingly large errors for excitation energies obtained with M06-2X. These errors are more than halved by restoring gauge invariance. The variable importance of imposing gauge invariance for different mGGA-based functionals can be rationalized by the derivative of the mGGA exchange energy integrand with respect to τ. In the second part, a large set of valence excitations in small main-group molecules is analyzed. For M06-2X, several selected n → π* and π→π$^{*}_{⊥}$ excitations are heavily gauge-dependent with average changes of –0.17 and –0.28 eV, respectively, while π→π$^{*}_{∥}$ excitations are marginally affected (–0.04 eV). Similar patterns, but of the opposite signs, are found for SCAN0. Here, the results suggest that reevaluation of previous gauge variant TDDFT results based on M06-2X and other mGGA functionals is warranted.

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

Molecular NMR shieldings, J -couplings, and magnetizabilities from numeric atom-centered orbital based density-functional calculations

This paper reports and benchmarks a new implementation of nuclear magnetic resonance shieldings, magnetizabilities, and J-couplings for molecules within semilocal density functional theory, based on numeric atom-centered orbital (NAO) basis sets. NAO basis sets are attractive for the calculation of these nuclear magnetic resonance (NMR) parameters because NAOs provide accurate atomic orbital representations especially near the nucleus, enabling high-quality results at modest computational cost. Moreover, NAOs are readily adaptable for linear scaling methods, enabling efficient calculations of large systems. Here, the paper has five main parts: (1) It reviews the formalism of density functional calculations of NMR parameters in one comprehensive text to make the mathematical background available in a self-contained way. (2) The paper quantifies the attainable precision of NAO basis sets for shieldings in comparison to specialized Gaussian basis sets, showing similar performance for similar basis set size. (3) The paper quantifies the precision of calculated magnetizabilities, where the NAO basis sets appear to outperform several established Gaussian basis sets of similar size. (4) The paper quantifies the precision of computed J-couplings, for which a group of customized NAO basis sets achieves precision of ~Hz for smaller basis set sizes than some established Gaussian basis sets. (5) The paper demonstrates that the implementation is applicable to systems beyond 1000 atoms in size.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules against the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.

Environmental Molecular Sciences Laboratory↗
NASA NTRS1984

The non-Gaussian joint probability density function of slope and elevation for a nonlinear gravity wave field

On the basis of the mapping method developed by Huang et al. (1983), an analytic expression for the non-Gaussian joint probability density function of slope and elevation for nonlinear gravity waves is derived. Various conditional and marginal density functions are also obtained through the joint density function. The analytic results are compared with a series of carefully controlled laboratory observations, and good agreement is noted. Furthermore, the laboratory wind wave field observations indicate that the capillary or capillary-gravity waves may not be the dominant components in determining the total roughness of the wave field. Thus, the analytic results, though derived specifically for the gravity waves, may have more general applications.

Huang, N. E.↗
DOE OSTI2016

Density functional theory based simulations of silicon nanowire field effect transistors

First-principles density functional theory (DFT) based, atomistic, self-consistent device simulations are performed for realistically sized Si nanowire field effect transistors (NW FETs) having tens of thousands of atoms. Through mode space transformation, DFT Hamiltonian and overlap matrices are reduced in size from a few thousands to around one hundred. Ultra-efficient quantum-mechanical transport calculations in the non-equilibrium Green's function formalism in a non-orthogonal basis are therefore made possible. The n-type and p-type Si NW FETs are simulated and found to exhibit similar device performance in the nanoscale regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2024

Toward 2D Dynamo Models Calibrated by Global 3D Relativistic Accretion Disk Simulations

Two-dimensional models assuming axisymmetry are an economical way to explore the long-term evolution of black hole accretion disks, but they are only realistic if the feedback of the nonaxisymmetric turbulence on the mean momentum and magnetic fields is incorporated. Dynamo terms added to the 2D induction equation should be calibrated to 3D MHD simulations. For generality, the dynamo tensors should be calibrated as functions of local variables rather than explicit functions of spatial coordinates in a particular basis. In this paper, we study the feedback of non-axisymmetric features on the 2D mean fields using a global 3D, relativistic, Cartesian simulation from the Illinois GRMHD code. We introduce new methods for estimating overall dynamo alpha and turbulent diffusivity effects as well as measures of the dominance of non-axisymmetric components of energies and fluxes within the disk interior. We attempt closure models of the dynamo EMF using least squares fitting, considering both models where coefficient tensors are functions of space and more global, covariant models. None of these models are judged satisfactory, but we are able to draw conclusions on what sorts of generalizations are and are not promising.

Matthew D Duez↗
DOE OSTI2016

Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist

Ca 2+ -sensing receptors (CaSRs) modulate calcium and magnesium homeostasis and many (patho)physiological processes by responding to extracellular stimuli, including divalent cations and amino acids. We report the first crystal structure of the extracellular domain (ECD) of human CaSR bound with Mg 2+ and a tryptophan derivative ligand at 2.1 Å. The structure reveals key determinants for cooperative activation by metal ions and aromatic amino acids. The unexpected tryptophan derivative was bound in the hinge region between two globular ECD subdomains, and represents a novel high-affinity co-agonist of CaSR. The dissection of structure-function relations by mutagenesis, biochemical, and functional studies provides insights into the molecular basis of human diseases arising from CaSR mutations. The data also provide a novel paradigm for understanding the mechanism of CaSR-mediated signaling that is likely shared by the other family C GPCR [G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptor] members and can facilitate the development of novel CaSR-based therapeutics.

Binding Affinity↗
NASA NTRS1987

Theoretical study of the dipole moment function of OH(X 2Pi)

A complete theoretical electric dipole moment function mu(r) is computed for OH(X 2Pi) at the full configuration-interaction (FCI) level for DZP + diffuse Gaussian basis set. The energy and dipole moment are also determined with 2d functions on oxygen at seven r values. The following methods are compared to the FCI for both the oxygen 1d and 2d basis sets: single-reference singles-plus-doubles configuration interaction (SDCI), SDCI with Davidson's correction, the coupled pair functional approach (CPF) and a modified form of CPF, CASSCF, and CASSCF-MRSDCI, and the external contracted CI(CCI) method. The dipole moments are evaluated both as an expectation value and by finite-field methods. The results support the superiority of evaluating the dipole moment as an energy derivative rather than as an expectation value.

Langhoff, Stephen R.↗
DOE OSTI2014

Theoretical predictions of properties and volatility of chlorides and oxychlorides of group-4 elements. II. Adsorption of tetrachlorides and oxydichlorides of Zr, Hf, and Rf on neutral and modified surfaces

With the aim to interpret results of gas-phase chromatography experiments on volatility of group-4 tetrachlorides and oxychlorides including those of Rf, adsorption enthalpies of these species on neutral, and modified quartz surfaces were estimated on the basis of relativistic, two-component Density Functional Theory calculations of MCl{sub 4}, MOCl{sub 2}, MCl{sub 6}{sup −}, and MOCl{sub 4}{sup 2} with the use of adsorption models. Several mechanisms of adsorption were considered. In the case of physisorption of MCl{sub 4}, the trend in the adsorption energy in the group should be Zr > Hf > Rf, so that the volatility should change in the opposite direction. The latter trend complies with the one in the sublimation enthalpies, ΔH{sub sub}, of the Zr and Hf tetrachlorides, i.e., Zr < Hf. On the basis of a correlation between these quantities, ΔH{sub sub}(RfCl{sub 4}) was predicted as 104.2 kJ/mol. The energy of physisorption of MOCl{sub 2} on quartz should increase in the group, Zr < Hf < Rf, as defined by increasing dipole moments of these molecules along the series. In the case of adsorption of MCl{sub 4} on quartz by chemical forces, formation of the MOCl{sub 2} or MOCl{sub 4}{sup 2−} complexes on the surface can take place, so that the sequence in the adsorption energy should be Zr > Hf > Rf, as defined by the complex formation energies. In the case of adsorption of MCl{sub 4} on a chlorinated quartz surface, formation of the MCl{sub 6}{sup 2−} surface complexes can occur, so that the trend in the adsorption strength should be Zr ≤ Hf < Rf. All the predicted sequences, showing a smooth change of the adsorption energy in the group, are in disagreement with the reversed trend Zr ≈ Rf < Hf, observed in the “one-atom-at-a-time” gas-phase chromatography experiments. Thus, currently no theoretical explanation can be found for the experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Some numerical calculations by using linear classical sonic theories approached from sub- or supersonic speeds

The unsteady aerodynamics of a two-dimensional wing at sonic speed are studied by using so-called classical sonic theories (linear), approached from supersonic flow (M=1+0) or subsonic flow (M=1-0). In the former approach, the exact expressions of lift and lift distribution are obtained in terms of Fresnel integrals, while in the latter approach an integral equation must be solved, the kernel function of which is obtained from the subsonic Possio's equation and has a root singularity. The discrete analysis is adopted on the basis of the semicircle method (SCM) and the weighting function for subsonic-flow-Gauss-quadrature, as well as modified characteristics obtained from both approaches agree quite well with each other. The results obtained by the present computations are compared with those of DLM-C (subsonic 2D code) developed by ANDO et al, and are found to give a reasonable outer boundary for subsonic unsteady aerodynamics.

Yamamoto, Y.↗
DOE OSTI2017

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation

The speckle-type POZ protein (SPOP) functions in the Cullin3-RING ubiquitin ligase (CRL3) as a receptor for the recognition of substrates involved in cell growth, survival, and signaling. SPOP mutations have been attributed to the development of many types of cancers, including prostate and endometrial cancers. Prostate cancer mutations localize in the substrate-binding site of the substrate recognition (MATH) domain and reduce or prevent binding. However, most endometrial cancer mutations are dispersed in seemingly inconspicuous solvent-exposed regions of SPOP, offering no clear basis for their cancer-causing and peculiar gain-of-function properties. Herein, we present the first structure of SPOP in its oligomeric form, uncovering several new interfaces important for SPOP self-assembly and normal function. Given that many previously unaccounted-for cancer mutations are localized in these newly identified interfaces, we uncover molecular mechanisms underlying dysregulation of SPOP function, with effects ranging from gross structural changes to enhanced self-association, and heightened stability and activity.

59 BASIC BIOLOGICAL SCIENCES↗