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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Adaptively Compressed Exchange Operator for Large-Scale Hybrid Density Functional Calculations with Applications to the Adsorption of Water on Silicene

Density functional theory (DFT) calculations using hybrid exchange-correlation functionals have been shown to provide an accurate description of the electronic structures of nanosystems. However, such calculations are often limited to small system sizes due to the high computational cost associated with the construction and application of the Hartree-Fock (HF) exchange operator. Here, we demonstrate that the recently developed adaptively compressed exchange (ACE) operator formulation [J. Chem. Theory Comput. 2016, 12, 2242-2249] can enable hybrid functional DFT calculations for nanosystems with thousands of atoms. The cost of constructing the ACE operator is the same as that of applying the exchange operator to the occupied orbitals once, while the cost of applying the Hamiltonian operator with a hybrid functional (after construction of the ACE operator) is only marginally higher than that associated with applying a Hamiltonian constructed from local and semilocal exchange-correlation functionals. Therefore, this new development significantly lowers the computational barrier for using hybrid functionals in large-scale DFT calculations. We demonstrate that a parallel planewave implementation of this method can be used to compute the ground-state electronic structure of a 1000-atom bulk silicon system in less than 30 wall clock minutes and that this method scales beyond 8000 computational cores for a bulk silicon system containing about 4000 atoms. The efficiency of the present methodology in treating large systems enables us to investigate adsorption properties of water molecules on Ag-supported two-dimensional silicene. Our computational results show that water monomer, dimer, and trimer configurations exhibit distinct adsorption behaviors on silicene. In particular, the presence of additional water molecules in the dimer and trimer configurations induces a transition from physisorption to chemisorption, followed by dissociation on Ag-supported silicene. This is caused by the enhanced effect of hydrogen bonds on charge transfer and proton transfer processes. Lastly, such a hydrogen bond autocatalytic effect is expected to have broad applications for silicene as an efficient surface catalyst for oxygen reduction reactions and water dissociation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

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

Accurate and Efficient ab Initio Calculations for Supramolecular Complexes: Symmetry-Adapted Perturbation Theory with Many-Body Dispersion

Symmetry-adapted perturbation theory (SAPT) provides a chemically meaningful energy decomposition scheme for nonbonded interactions that is useful for interpretive purposes. Although formally a dimer theory, we have previously introduced an “extended” version (XSAPT) that incorporates many-body polarization via self-consistent charge embedding. Here, we extend the XSAPT methodology to include nonadditive dispersion, using a modified form of the many-body dispersion (MBD) method of Tkatchenko and co-workers. Dispersion interactions beyond the pairwise atom–atom approximation improve total interaction energies even in small systems, and for large π-stacked complexes these corrections can amount to several kilocalories per mole. The XSAPT+MBD method introduced here achieves errors of ≲1 kcal/mol (as compared to high-level ab initio benchmarks) for the L7 data set of large dispersion-bound complexes and ≲4 kcal/mol (as compared to experiment) for the S30L data set of host–guest complexes. This is superior to the best contemporary density functional methods for noncovalent interactions, at comparable or lower cost. XSAPT+MBD represents a promising method for application to supramolecular assemblies, including protein–ligand binding.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2013

Structure of Stoichiometric and Oxygen-Rich Ultrathin FeO(111) Films Grown on Pd(111)

Monolayer thin FeO(111) films were grown on Pd(111) and oxidized by atomic oxygen (O). The stoichiometric and oxidized films were studied in detail by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Compared to the previously studied FeO(111)/Pt(111) system, small structural differences were observed for stoichiometric FeO monolayer films. Upon O exposure, the stoichiometric FeO film reconstructs, leading to the formation of new O-rich structures incorporating increasing amounts of additional O atoms. At low O exposures, the STM images exhibit bright features of regularly sized triangular structures assigned to O-adatom dislocation loops. A model of this O-rich structure composed of four-fold O-coordinated Fe atoms is proposed and confirmed by DFT calculations. Furthermore, these O dislocation loops induce the inversion of the FeO film and enclose portions of the film in which the order of the high-symmetry domains is inverted. For higher O exposures, the formation of FeO 2–x islands coexisting with O-adatom dislocations and stoichiometric FeO patches was observed. Finally, these FeO 2–x islands are reminiscent of the O-rich structures previously reported for FeO supported on Pt(111) and are catalytically active toward CO oxidation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Interplay between plasmon and single-particle excitations in a metal nanocluster

Plasmon-generated hot carriers are used in photovoltaic or photochemical applications. However, the interplays between the plasmon and single-particle excitations in nanosystems have not been theoretically addressed using ab initio methods. Here we show such interplays in a Ag 55 nanocluster using real-time time-dependent density functional theory simulations. We find that the disappearance of the zero-frequency peak in the Fourier transform of the band-to-band transition coefficient is a hallmark of the plasmon. We show the importance of the d-states for hot-carrier generations. If the single-particle d-to-s excitations are resonant to the plasmon frequency, the majority of the plasmon energy will be converted into hot carriers, and the overall hot-carrier generation is enhanced by the plasmon; if such resonance does not exist, we observe an intriguing Rabi oscillation between the plasmon and hot carriers. Phonons play a minor role in plasmonic dynamics in such small systems. Ultimately, this study provides guidance on improving plasmonic applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Predicting electronic structures at any length scale with machine learning

The properties of electrons in matter are of fundamental importance. They give rise to virtually all material properties and determine the physics at play in objects ranging from semiconductor devices to the interior of giant gas planets. Modeling and simulation of such diverse applications rely primarily on density functional theory (DFT), which has become the principal method for predicting the electronic structure of matter. While DFT calculations have proven to be very useful, their computational scaling limits them to small systems. We have developed a machine learning framework for predicting the electronic structure on any length scale. It shows up to three orders of magnitude speedup on systems where DFT is tractable and, more importantly, enables predictions on scales where DFT calculations are infeasible. Our work demonstrates how machine learning circumvents a long-standing computational bottleneck and advances materials science to frontiers intractable with any current solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

An analytical model of “Electron-Only” magnetic reconnection rates

Abstract “Electron-only” reconnection, which is both uncoupled from the surrounding ions and much faster than standard reconnection, is arguably ubiquitous in turbulence. One critical step to understanding the rate in this novel regime is to model the outflow speed that limits the transport of the magnetic flux, which is super ion Alfvénic but significantly lower than the electron Alfvén speed based on the asymptotic reconnecting field. Here we develop a simple model to determine this limiting speed by taking into account the multiscale nature of reconnection, the Hall-mediated electron outflow speed, and the pressure buildup within the small system. The predicted scalings of rates and various key quantities compare well with fully kinetic simulations and can be useful for interpreting the observations of NASA’s Magnetospheric-Multiscale (MMS) mission and other ongoing missions.

Physics↗
DOE OSTI2011

Nanostructured Electrodes For Organic Bulk Heterojunction Solar Cells: Model Study Using Carbon Nanotube Dispersed Polythiophene-fullerene Blend Devices

We test the feasibility of using nanostructured electrodes in organic bulk heterojunction solar cells to improve their photovoltaic performance by enhancing their charge collection efficiency and thereby increasing the optimal active blend layer thickness. As a model system, small concentrations of single wall carbon nanotubes are added to blends of poly(3-hexylthiophene): [6,6]-phenyl-C{sub 61}-butyric acid methyl ester in order to create networks of efficient hole conduction pathways in the device active layer without affecting the light absorption. The nanotube addition leads to a 22% increase in the optimal blend layer thickness from 90 nm to 110 nm, enhancing the short circuit current density and photovoltaic device efficiency by as much as {approx}10%. The associated incident-photon-to-current conversion efficiency for the given thickness also increases by {approx}10% uniformly across the device optical absorption spectrum, corroborating the enhanced charge carrier collection by nanostructured electrodes.

14 SOLAR ENERGY↗
DOE OSTI2012

Implementation of the multireference Brillouin-Wigner and Mukherjee’s coupled cluster methods with non-iterative triple excitations utilizing reference-level parallelism

In this paper we discuss the performance of the non-iterative State-Specific Mul- tireference Coupled Cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with the exact full configuration interaction results (FCI) for small systems (H2O, N2, and Be3). For larger systems (naphthyne isomers and -carotene), the non-iterative BW-MRCCSD(T) and Mk-MRCCSD(T) methods are compared against the results obtained with the single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of pro- cessor groups.

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

Fundamental gaps with approximate density functionals: The derivative discontinuity revealed from ensemble considerations

The fundamental gap is a central quantity in the electronic structure of matter. Unfortunately, the fundamental gap is not generally equal to the Kohn-Sham gap of density functional theory (DFT), even in principle. The two gaps differ precisely by the derivative discontinuity, namely, an abrupt change in slope of the exchange-correlation energy as a function of electron number, expected across an integer-electron point. Popular approximate functionals are thought to be devoid of a derivative discontinuity, strongly compromising their performance for prediction of spectroscopic properties. Here we show that, in fact, all exchange-correlation functionals possess a derivative discontinuity, which arises naturally from the application of ensemble considerations within DFT, without any empiricism. This derivative discontinuity can be expressed in closed form using only quantities obtained in the course of a standard DFT calculation of the neutral system. For small, finite systems, addition of this derivative discontinuity indeed results in a greatly improved prediction for the fundamental gap, even when based on the most simple approximate exchange-correlation density functional – the local density approximation (LDA). For solids, the same scheme is exact in principle, but when applied to LDA it results in a vanishing derivative discontinuity correction. This failure is shown to be directly related to the failure of LDA in predicting fundamental gaps from total energy differences in extended systems.

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

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behavior of large systems or to perform systematic scans of smaller systems. While powerful algorithms are available to facilitate the sampling of the conformational space, successful applications of such models are hindered by the availability of simple enough potentials able to satisfactorily reproduce known properties of the system. We develop an interatomic potential to account for a number of properties of proteins in a computationally economic way. The potential is defined within an all-atom, implicit solvent model by contact functions between the different atom types. The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that they are expressible as thermal averages of some conformational properties. We test this model on three different proteins, for which we also perform a scan of all possible point mutations with explicit conformational sampling. The resulting models, optimized solely on a subset of native distances, not only reproduce the native conformations within a few Angstroms from the experimental ones, but show the cooperative transition between native and denatured state and correctly predict the measured free-energy changes associated with point mutations. Moreover, differently from other structure-based models, our method leaves a residual degree of frustration, which is known to be present in protein molecules.

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

Approaching exact hyperpolarizabilities via sum-over-states Monte Carlo configuration interaction

We propose using sum-over-states calculations with the compact wavefunctions of Monte Carlo configuration interaction to approach accurate values for higher-order dipole properties up to second hyperpolarizabilities in a controlled way. We apply the approach to small systems that can generally be compared with full configuration interaction (FCI) results. We consider hydrogen fluoride with a 6-31g basis and then look at results, including frequency dependent properties, in an aug-cc-pVDZ basis. We extend one calculation beyond FCI by using an aug-cc-pVTZ basis. The properties of an H{sub 4} molecule with multireference character are calculated in an aug-cc-pVDZ basis. We then investigate this method on a strongly multireference system with a larger FCI space by modelling the properties of carbon monoxide with a stretched geometry. The behavior of the approach with increasing basis size is considered by calculating results for the neon atom using aug-cc-pVDZ to aug-cc-pVQZ. We finally test if the unusual change in polarizability between the first two states of molecular oxygen can be reproduced by this method in a 6-31g basis.

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

Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

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

A universal preconditioner for simulating condensed phase materials

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

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

Stochastic lag time in nucleated linear self-assembly

Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise on account of the small system size at the cellular scale. We study the nucleated reversible self-assembly of monomeric building blocks into polymer-like aggregates using the method of kinetic Monte Carlo. Kinetic Monte Carlo, being inherently stochastic, allows us to study the impact of fluctuations on the polymerization reactions. One of the most important characteristic features in this kind of problem is the existence of a lag phase before self-assembly takes off, which is what we focus attention on. We study the associated lag time as a function of system size and kinetic pathway. We find that the leading order stochastic contribution to the lag time before polymerization commences is inversely proportional to the system volume for large-enough system size for all nine reaction pathways tested. Finite-size corrections to this do depend on the kinetic pathway.

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

Insights on finite size effects in ab initio study of CO adsorption and dissociation on Fe 110 surface

Adsorption and dissociation of hydrocarbons on metallic surfaces represent crucial steps on the path to carburization, eventually leading to dusting corrosion. While adsorption of CO molecules on Fe surface is a barrier-less exothermic process, this is not the case for the dissociation of CO into C and O adatoms and the diffusion of C beneath the surface that are found to be associated with large energy barriers. In practice, these barriers can be affected by numerous factors that combine to favour the CO-Fe reaction such as the abundance of CO and other hydrocarbons as well as the presence of structural defects. From a numerical point of view, studying these factors is challenging and a step-by-step approach is necessary to assess, in particular, the influence of the finite box size on the reaction parameters for adsorption and dissociation of CO on metal surfaces. Here, we use density functional theory (DFT) total energy calculations with the climbing-image nudged elastic band method to estimate the adsorption energies and dissociation barriers for different CO coverages with surface supercells of different sizes. We further compute the effect of periodic boundary condition for DFT calculations and find that the contribution from van der Waals interaction in the computation of adsorption parameters is important as they contribute to correcting the finite-size error in small systems. The dissociation process involves carbon insertion into the Fe surface causing a lattice deformation that requires a larger surface system for unrestricted relaxation. We show that, in the larger surface systems associated with dilute CO-coverages, C-insertion is energetically more favourable, leading to a significant decrease in the dissociation barrier. This observation suggests that a large surface system with dilute coverage is necessary for all similar metal-hydrocarbon reactions in order to study their fundamental electronic mechanisms, as an isolated phenomenon, free from finite-size effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Stochastic resolution of identity second-order Matsubara Green’s function theory

We create a stochastic resolution of identity representation to the second-order Matsubara Green’s function (sRI-GF2) theory. Using a stochastic resolution of the Coulomb integrals, the second order Born self-energy in GF2 is decoupled and reduced to matrix products/ contractions, which reduces the computational cost from O(N 5 ) to O(N 3 ) (with N being the number of atomic orbitals). Currently, the method can be viewed as an extension to our previous work on stochastic resolution of identity second order Møller-Plesset perturbation theory [T. Y. Takeshita et al., J. Chem. Theory Comput. 13, 4605 (2017)] and offers an alternative to previous stochastic GF2 formulations [D. Neuhauser et al., J. Chem. Theory Comput. 13, 5396 (2017)]. We show that sRI-GF2 recovers the deterministic GF2 results for small systems, is computationally faster than deterministic GF2 for N > 80, and is a practical approach to describe weak correlations in systems with 10 3 electrons and more.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗