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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34

Ubiquitin (Ub) signaling requires the sequential interactions and activities of three enzymes, E1, E2, and E3. Cdc34 is an E2 that plays a key role in regulating cell cycle progression and requires unique structural elements to function. The molecular basis by which Cdc34 engages its E1 and the structural mechanisms by which its unique C-terminal extension functions in Cdc34 activity are unknown. Here, we present crystal structures of Cdc34 alone and in complex with E1, and a Cdc34~Ub thioester mimetic that represents the product of Uba1-Cdc34 Ub transthiolation. These structures reveal conformational changes in Uba1 and Cdc34 and a unique binding mode that are required for transthiolation. The Cdc34~Ub structure reveals contacts between the Cdc34 C-terminal extension and Ub that stabilize Cdc34~Ub in a closed conformation and are critical for Ub discharge. Altogether, our structural, biochemical, and cell-based studies provide insights into the molecular mechanisms by which Cdc34 function in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Vibrationally resolved NEXAFS at C and N K-edges of pyridine, 2-fluoropyridine and 2,6-difluoropyridine: A combined experimental and theoretical assessment

In the present work, the near edge X-ray absorption spectroscopy (NEXAFS) spectra at both C and N K-edges of pyridine, 2-fluoropyridine, and 2,6-difluoropyridine have been studied both experimentally and theoretically. From an electronic point of view, both transition potential density functional theory and time-dependent density functional theory approaches lead to reliable results provided that suitable basis sets and density functionals are employed. In this connection, the global hybrid B3LYP functional in conjunction with the EPR-III basis set appears particularly suitable after constant scaling of the band positions. For the N K-edge, vertical energies obtained at these levels and broadened by symmetric Gaussian distributions provide spectra in reasonable agreement with the experiment. Vibronic contributions further modulate the band-shapes leading to a better agreement with the experimental results, but are not strictly necessary for semi-quantitative investigations. On the other hand, vibronic contributions are responsible for strong intensity redistribution in the NEXAFS C K-edge spectra, and their inclusion is thus mandatory for a proper description of experiments. In this connection, the simple vertical gradient model is particularly appealing in view of its sufficient reliability and low computational cost. For more quantitative results, the more refined vertical Hessian approach can be employed, and its effectiveness has been improved thanks to a new least-squares fitting approach.

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

An efficient extrapolation to the (T)/CBS limit

We extrapolate to the perturbative triples (T)/complete basis set (CBS) limit using double ζ basis sets without polarization functions (Wesleyan-1-Triples-2ζ or “Wes1T-2Z”) and triple ζ basis sets with a single level of polarization functions (Wesleyan-1-Triples-3ζ or “Wes1T-3Z”). These basis sets were optimized for 102 species representing the first two rows of the Periodic Table. The species include the entire set of neutral atoms, positive and negative atomic ions, as well as several homonuclear diatomic molecules, hydrides, rare gas dimers, polar molecules, such as oxides and fluorides, and a few transition states. The extrapolated Wes1T-(2,3)Z triples energies agree with (T)/CBS benchmarks to within ±0.65 mE{sub h}, while the rms deviations of comparable model chemistries W1, CBS-APNO, and CBS-QB3 for the same test set are ±0.23 mE{sub h}, ±2.37 mE{sub h}, and ±5.80 mE{sub h}, respectively. The Wes1T-(2,3)Z triples calculation time for the largest hydrocarbon in the G2/97 test set, C{sub 6}H{sub 5}Me{sup +}, is reduced by a factor of 25 when compared to W1. The cost-effectiveness of the Wes1T-(2,3)Z extrapolation validates the usefulness of the Wes1T-2Z and Wes1T-3Z basis sets which are now available for a more efficient extrapolation of the (T) component of any composite model chemistry.

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

An efficient basis set representation for calculating electrons in molecules

The method of McCurdy, Baertschy, and Rescigno, is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O( N log (N)) multiplication operations, not O( N 4 ), where N is the number of basis functions; N = n 3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He + , H + 2 ), 2- (H 2 , He), 10- (CH 4 ), and 56-electron (C 8 H 8 ) systems.

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

First-principles study of the infrared spectrum in liquid water from a systematically improved description of H-bond network

An accurate ab initio theory of the H-bond structure of liquid water requires a high-level exchange correlation approximation from density functional theory. Based on the liquid structures modeled by ab initio molecular dynamics by using maximally localized Wannier functions as a basis, we study the infrared spectrum of water within the canonical ensemble. In particular, we employ both the Perdew-Burke-Ernzerhof (PBE) functional within the generalized gradient approximation (GGA) and the state-of-the-art meta-GGA level approximation provided by the strongly constrained and appropriately normed (SCAN) functional. In this work, we demonstrate that the SCAN functional improves not only the water structure but also the theoretical infrared spectrum of water. Our analyses show that the improvement in the stretching and bending bands can be mainly attributed to better descriptions of directional H bonding and the covalency at the inter- and intramolecular levels, respectively. On the other hand, better agreements in libration and hindered translation bands are due to the improved dynamics of the H-bond network enabled by a less structured liquid in the experimental direction. The spectrum predicted by SCAN shows much better agreement with experimental data than the conventionally widely adopted PBE functional at the GGA level.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Nuclear-electronic orbital reduced explicitly correlated Hartree-Fock approach: Restricted basis sets and open-shell systems

The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF{sup −} and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN{sup +}, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.

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

Modeling the diffusion of heat energy within composites of homogeneous materials using the uncertainty principle

The goal of this paper is to develop a highly accurate and efficient numerical method for the solution of a time-dependent partial differential equation with a piecewise constant coefficient, on a finite interval with periodic boundary conditions. The resulting algorithm can be used, for example, to model the diffusion of heat energy in one space dimension, in the case where the spatial domain represents a medium consisting of two homogeneous materials. The resulting model has, to our knowledge, not yet been solved in closed form through analytical methods, and is difficult to solve using existing numerical methods, thus suggesting an alternative approach. The approach presented in this paper is to represent the solution as a linear combination of wave functions that change frequencies at the interfaces between different materials. It is demonstrated through numerical experiments that using the Uncertainty Principle to construct a basis of such functions, in conjunction with a spectral method, a mathematical model for heat diffusion through different materials can be solved much more efficiently than with conventional time-stepping methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Enabling attractive-repulsive potentials in binary-collision-approximation monte-carlo codes for ion-surface interactions

Abstract Binary Collision Approximation (BCA) codes for ion-material interactions, such as SRIM, Tridyn, F-TRIDYN, and SDtrimSP, have historically been limited to screened Coulomb potentials even at low energies due to the difficulty in numerically solving the Distance of Closest Approach (DOCA) problem for attractive-repulsive potentials. Techniques such as direct n-body simulation or modifications to Newton’s method are either prohibitively costly or not guaranteed to work for all potentials. Advanced rootfinding techniques, such as companion matrix solvers, offer a solution. For many attractive-repulsive potentials, however, a companion matrix cannot be used directly, because there is no way to put the associated functions into a monomial basis form. A complementary technique is proxy rootfinding—by finding the best-fit polynomial approximant of a function, the zeros of the approximant can be guaranteed to be close to the zeros of the function. Using the Chebyshev basis and grid offers additional guarantees with regards to the quality of the approximation, the speed of convergence, and the avoidance of Runge’s phenomenon. By finding Chebyshev interpolants and using the Chebyshev-Frobenius companion matrix, the zeros of any real function on a bounded domain can be found. Here we show that using an Adaptive Chebyshev Proxy Rootfinder with Automatic Subdivision (ACPRAS) with appropriate scaling functions, numerical issues presented by attractive-repulsive potentials, including those of scale, can be handled. Using these techniques, we show that it is possible to include any physically reasonable interatomic potential in a BCA code, and to guarantee correctness of the resulting scattering angle calculations.

Materials Science↗
DOE OSTI2024

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ~400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reproducibility of calculations on Li species with correlation-consistent basis sets

Here we have found that two different basis set series, both labeled cc-pVxZ, are widely available and widely used for calculation on Li compounds such that calculations that should be the same are different, causing a reproducibility problem. Here we study the magnitude of the disagreement of these nominally-the-same basis sets for wave function and density functional calculations of Li clusters. We find deviations among the basis sets of as large as 22 millihartrees. In most cases one obtains lower energies with the noncanonical choices. Therefore, it is important to specify which version of the basis set is used for calculations.

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

HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160

HVEM is a TNF (tumor necrosis factor) receptor contributing to a broad range of immune functions involving diverse cell types. It interacts with a TNF ligand, LIGHT, and immunoglobulin (Ig) superfamily members BTLA and CD160. Assessing the functional impact of HVEM binding to specific ligands in different settings has been complicated by the multiple interactions of HVEM and HVEM binding partners. To dissect the molecular basis for multiple functions, we determined crystal structures that reveal the distinct HVEM surfaces that engage LIGHT or BTLA/CD160, including the human HVEM–LIGHT–CD160 ternary complex, with HVEM interacting simultaneously with both binding partners. Based on these structures, we generated mouse HVEM mutants that selectively recognized either the TNF or Ig ligands in vitro. Knockin mice expressing these muteins maintain expression of all the proteins in the HVEM network, yet they demonstrate selective functions for LIGHT in the clearance of bacteria in the intestine and for the Ig ligands in the amelioration of liver inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

57Fe Mössbauer isomer shift of pure iron and iron oxides at high pressure—An experimental and theoretical study

The 57Fe isomer shift (IS) of pure iron has been measured up to 100 GPa using synchrotron Mössbauer spectroscopy in the time domain. Apart from the expected discontinuity due to the α→ε structural and spin transitions, the IS decreases monotonically with increasing pressure. The absolute shifts were reproduced without semi-empirical calibrations by periodic density functional calculations employing extensive localized basis sets with several common density functionals. However, the best numerical agreement is obtained with the B1WC hybrid functional. Extension of the calculations to 350 GPa, a pressure corresponding to the Earth’s inner core, predicted the IS range of 0.00 to -0.85 mm/s, covering the span from Fe(0) to Fe(VI) compounds measured at ambient pressure. The calculations also reproduced the pressure trend from polymorphs of prototypical iron oxide minerals, FeO and Fe2O3. Analysis of the electronic structure shows a strong donation of electrons from oxygen to iron at high pressure. The assignment of formal oxidation to the Fe atom becomes ambiguous under this condition.

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

Crossing symmetry, transcendentality and the Regge behaviour of 1d CFTs

We develop the technology for Polyakov-Mellin (PM) bootstrap in one- dimensional conformal field theories (CFT 1 ). By adding appropriate contact terms, we bootstrap various effective field theories in AdS 2 and analytically compute the CFT data to one loop. The computation can be extended to higher orders in perturbation theory, if we ignore mixing, for any external dimension. We develop PM bootstrap for O(N) theories and derive the necessary contact terms for such theories (which also involves a new higher gradient contact term absent for N = 1). We perform cross-checks which include considering the diagonal limit of the 2d Ising model in terms of the 1d PM blocks. As an independent check of the validity of the results obtained with PM bootstrap, we propose a suitable basis of transcendental functions, which allows to fix the four-point correlators of identical scalar primaries completely, up to a finite number of ambiguities related to the number of contact terms in the PM basis. We perform this analysis both at tree level (with and without exchanges) and at one loop. We also derive expressions for the corresponding CFT data in terms of harmonic sums. Finally, we consider the Regge limit of one-dimensional correlators and derive a precise connection between the latter and the large-twist limit of CFT data. Exploiting this result, we study the crossing equation in the three OPE limits and derive some universal constraints for the large-twist limit of CFT data in Regge-bounded theories with a finite number of exchanges.

1/N expansion↗
DOE OSTI2021

encore : an O ( N g2) estimator for galaxy N -point correlation functions

ABSTRACT We present a new algorithm for efficiently computing the N-point correlation functions (NPCFs) of a 3D density field for arbitrary N. This can be applied both to a discrete spectroscopic galaxy survey and a continuous field. By expanding the statistics in a separable basis of isotropic functions built from spherical harmonics, the NPCFs can be estimated by counting pairs of particles in space, leading to an algorithm with complexity $\mathcal {O}(N_\mathrm{g}^2)$ for Ng particles, or $\mathcal {O}(N_\mathrm{FFT}\log N_\mathrm{FFT})$ when using a Fast Fourier Transform with NFFT grid-points. In practice, the rate-limiting step for N > 3 will often be the summation of the histogrammed spherical harmonic coefficients, particularly if the number of radial and angular bins is large. In this case, the algorithm scales linearly with Ng. The approach is implemented in the encore code, which can compute the 3PCF, 4PCF, 5PCF, and 6PCF of a BOSS-like galaxy survey in ${\sim}100$ CPU-hours, including the corrections necessary for non-uniform survey geometries. We discuss the implementation in depth, along with its GPU acceleration, and provide practical demonstration on realistic galaxy catalogues. Our approach can be straightforwardly applied to current and future data sets to unlock the potential of constraining cosmology from the higher point functions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A discontinuous piecewise polynomial generalized moving least squares scheme for robust finite element analysis on arbitrary grids

A variational approach is developed with a meshless discretization to enable accurate and robust numerical simulation of partial differential equations for meshes that are of poor quality. Traditional finite element methods use the mesh to both discretize the geometric domain and to define the finite element shape functions. The latter creates a dependence between the quality of the mesh and the properties of the finite element basis that may adversely affect the accuracy of the discretized problem. Here, we propose a new approach for defining finite element shape functions that breaks this dependence and separates mesh quality from the discretization quality, which we call discontinuous piecewise polynomial generalized moving least squares (DPP-GMLS). At the core of the approach is a meshless definition of the shape functions, which limits the purpose of the mesh to representing the geometric domain and integrating the basis functions without having any role in their approximation quality. The resulting non-conforming space can be utilized within a standard discontinuous Galerkin framework, providing a rigorous foundation for solving partial differential equations on low-quality meshes. We present a collection of numerical experiments demonstrating our approach in a wide range of settings: strongly coercive elliptic problems, linear elasticity in the compressible regime, and the stationary Stokes problem. We demonstrate convergence for all problems and stability for element pairs for problems which usually require inf-sup compatibility for conforming methods, also referring to a minor modification possible through the symmetric interior penalty Galerkin framework for stabilizing element pairs that would otherwise be traditionally unstable. Mesh robustness is particularly critical for elasticity, and we provide an example that our approach provides a greater than 5 x improvement in accuracy and allows for taking an 8 x larger stable timestep for a highly deformed mesh, compared to the continuous Galerkin finite element method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Efficient Calculation of NMR Shielding Constants Using Composite Method Approximations and Locally Dense Basis Sets

This paper presents a systematic study of applying composite method approximations with locally dense basis sets (LDBS) to efficiently calculate NMR shielding constants in small and medium-sized molecules. The pcSseg-n series of basis sets are shown to have similar accuracy to the pcS-n series when n ≥ 1 and can slightly reduce computational costs. We identify two different LDBS partition schemes that perform very effectively for density functional calculations. Here, we select a large subset of the recent NS372 database containing 290 H, C, N, and O shielding values evaluated by reference methods on 106 molecules to carefully assess methods of the high, medium, and low computational costs to make practical recommendations. Our assessment covers conventional electronic structure methods (density functional theory and wave function) with global basis calculations, as well as their use in one of the satisfactory LDBS approaches, and a range of composite approaches, also with and without LDBS. Altogether 99 methods are evaluated. On this basis, we recommend different methods to reach three different levels of accuracy and time requirements across the four nuclei considered.

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

Molecular electric moments calculated by using natural orbital functional theory

The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods.

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

Regression Based Approach for Robust Finite Element Analysis on Arbitrary Grids. LDRD Final Report

This report summarizes the work performed under a one-year LDRD project aiming to enable accurate and robust numerical simulation of partial differential equations for meshes that are of poor quality. Traditional finite element methods use the mesh to both discretize the geometric domain and to define the finite element shape functions. The latter creates a dependence between the quality of the mesh and the properties of the finite element basis that may adversely affect the accuracy of the discretized problem. In this project, we propose a new approach for defining finite element shape functions that breaks this dependence and separates mesh quality from the discretization quality. At the core of the approach is a meshless definition of the shape functions, which limits the purpose of the mesh to representing the geometric domain and integrating the basis functions without having any role in their approximation quality. The resulting non-conforming space can be utilized within a standard discontinuous Galerkin framework providing a rigorous foundation for solving partial differential equations on low-quality meshes. We present a collection of numerical experiments demonstrating our approach in a wide range of settings: strongly coercive elliptic problems, linear elasticity in the compressible regime, and the stationary Stokes problem. We demonstrate convergence for all problems and stability for element pairs for problems which usually require inf-sup compatibility for conforming methods, also referring to a minor modification possible through the symmetric interior penalty Galerkin framework for stabilizing element pairs that would otherwise be traditionally unstable. Mesh robustness is particularly critical for elasticity, and we provide an example that our approach provides a greater than 5x improvement in accuracy and allows for taking an 8x larger stable timestep for a highly deformed mesh, compared to the continuous Galerkin finite element method. The report concludes with a brief summary of ongoing projects and collaborations that utilize or extend the products of this work.

97 MATHEMATICS AND COMPUTING↗