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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations

The representation and storage of two-electron integral tensors are vital in large- scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this paper, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of atomic basis set N_b ranging from ~ 100 up to ~ 2, 000, the observed numerical scaling of our implementation shows O(N_b^{2.5~3}) versus O(N_b^{3~4}) of single CD in most of other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic-orbital (AO) two-electron integral tensor from O(N_b^4) to O(N_b^2 log_{10}(N_b)) with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled- cluster formalism employing single and double excitations (CCSD) on several bench- mark systems including the C_{60} molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10^{-4} to 10^{-3} to give acceptable compromise between efficiency and accuracy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Nonadiabatic Dynamics of Photoexcited cis-Stilbene Using Ab Initio Multiple Spawning

The photochemistry of cis-stilbene proceeds through two pathways: cis-trans isomerization and ring closure to 4a,4b-dihydrophenanthrene (DHP). Despite serving for many decades as a model system for photoisomerization, the photodynamics of cis-stilbene is still not fully understood. In this work, we use ab initio multiple spawning on a SA-2-CASSCF(2,2) potential energy surface to simulate the nonadiabatic dynamics of isolated cis-stilbene. We find the cyclization (to DHP and cis-stilbene) and isomerization (to trans- and cis-stilbene) reaction coordinates to be orthogonal; branching between the two pathways is determined on the S1 excited state within 150 fs of photoexcitation. Furthermore ,trajectory basis functions (TBFs) undergoing cyclization decay rapidly to the ground state in 250 fs, while TBFs moving along the isomerization coordinate remain on the excited state longer, with the majority decaying between 300 and 500 fs. We observe three avoided crossing regions in the dynamics: two along the isomerization coordinate (displaying pyramidalization and migration of an ethylenic hydrogen or phenyl group), and one DHP-like conical intersection along the cyclization coordinate. The isomeric form of the vibrationally hot photoproducts (as determined by measurement 2 ps after photoexcitation) is determined within less than 50 fs of decay to the ground state mediated by passage through a conical intersection. Excess vibrational energy of ground state cis- and trans-stilbene is channelled into phenyl torsions (with mostly opposing directionality). Finally, our simulations are validated by direct comparison to experiment for the absorption spectrum, branching ratio of the three photoproducts (44:52:4 cis-stilbene:trans-stilbene:DHP), and excited state lifetime (520 ± 40 fs).

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

Quantifying Errors in Effective Cluster Interactions of Lattice Gas Cluster Expansions

The promise of lattice gas (LG) cluster expansions (CEs) is that they can describe a given system property to any level of accuracy since the orthogonal “cluster basis functions” span the complete space of available configurations. Such an approach can be constructed to an arbitrarily large surface of a finite number of distinct adsorption sites. Unfortunately, this is only true for the case of an ideal, fixed lattice decorated with components at precise lattice points (the lattice “sites”) with no distortions or relaxations subsequently allowed. Since most systems, and surfaces specifically, do not conform to such an ideal set of constraints, errors in LG CEs must be expected or CE convergence severely hampered. Beyond this, numerical errors in the provided data can complicate the proper construction of a truly predictive and/or physically significant CE. In this work, we show here how reliance on typical statistical tools like confidence intervals cannot be expected to provide an accurate representation of the uncertainty of effective cluster interactions (ECIs) in the CE due to the nature of the target ab initio data and the nature of CEs themselves. We develop a method for estimating these errors that does not rely on statistical assumptions about the model or data. We then use these ECI errors to quantify fundamental consequences on the uncertainty of ECIs in CEs built from O/Fe(100) data whose surface and adsorbates have been allowed to relax in a typical manner and from O/Fe(100) data whose surface and adsorbates are fixed in ideal lattice positions. We also quantify the effect of using a different density functional theory exchange–correlation functional, using these ECI errors to assess the significance in any deviations. In both cases, our method is shown to have remarkable utility in the quantification of errors in the ECIs of CEs. While we stick to the lattice gas convention in this work, the method is equally applicable to the Ising convention or, in principle, any linear model of sufficient complexity.

08 HYDROGEN↗
DOE OSTI2016

Theory of Exciton Energy Transfer in Carbon Nanotube Composites

Here, we compute the exciton transfer (ET) rate between semiconducting single-wall carbon nanotubes (SWNTs). We show that the main reasons for the wide range of measured ET rates reported in the literature are (1) exciton confinement in local quantum wells stemming from disorder in the environment and (2) exciton thermalization between dark and bright states due to intratube scattering. The SWNT excitonic states are calculated by solving the Bethe–Salpeter equation using tight-binding basis functions. The ET rates due to intertube Coulomb interaction are computed via Fermi’s golden rule. In pristine samples, the ET rate between parallel (bundled) SWNTs of similar chirality is very high (~10 14 s –1 ), while the ET rate for dissimilar or nonparallel tubes is considerably lower (~10 12 s –1 ). Exciton confinement reduces the ET rate between same-chirality parallel SWNTs by 2 orders of magnitude but has little effect otherwise. Consequently, the ET rate in most measurements will be on the order of 10 12 s –1 , regardless of the tube relative orientation or chirality. Exciton thermalization between bright and dark states further reduces the ET rate to ~10 11 s –1 . The ET rate also increases with increasing temperature and decreases with increasing dielectric constant of the surrounding medium.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Guest-Host Interactions in Clathrate Hydrates: Benchmark MP2 and CCSD(T)/CBS Binding Energies of CH4, CO2 and H2S in (H2O)20 Cages

We present benchmark binding energies of naturally occurring gas molecules CH4, CO2, and H2S in the small cage, namely the pentagonal dodecahedron (512) (H2O)20, which is one of the constituent cages of the 3 major lattices (structures I, II and H) of clathrate hydrates. These weak interactions require higher levels of electron correlation and converge slowly with increasing basis set to the Complete Basis Set (CBS) limit, necessitating the use of large basis sets up to the augcc- pV5Z and subsequent correction for Basis Set Superposition Error (BSSE). For the host hollow (H2O)20 cages we have identified a most stable isomer with binding energy of -200.8 ± 2.1 kcal/mol at the CCSD(T)/CBS limit (-199.2 ± 0.5 kcal/mol at the MP2/CBS limit). Additionally, we report converged second order Moller-Plesset (MP2) CBS binding energies for the encapsulation of guests in the (H2O)20 cage of -4.3 ± 0.1 for CH4@(H2O)20, -6.6 ± 0.1 for CO2@(H2O)20 and -8.5 ± 0.1 kcal/mol for H2S@(H2O)20, respectively. For CH4@(H2O)20, exhibiting the weakest encapsulation affinity among the three, we report CCSD(T)/aug-cc-pVTZ binding energies and, based on them, a CCSD(T)/CBS estimate of -4.75 ± 0.1 kcal/mol. To the best of our knowledge, the CCSD(T)/aug-cc-pVTZ calculation for CH4@(H2O)20 is the largest one reported to date (168 valence electrons, 1978 basis functions and the correlation of 84 doubly occupied and 1873 virtual orbitals) and required a scalable implementation of the (T) module on 6144 nodes (350208 cores) of the “Cori” supercomputer at the National Energy Research Supercomputing Center (NERSC) for a total execution time of 195 minutes (for the (T) part). These efficient scalable implementations of highly correlated methods offer the capability to obtain long-lasting benchmarks of intermolecular interactions in complex systems. They also provide a path towards parametrizing classical potentials needed to study the dynamical and transport properties in these complex systems as well as assess the accuracy of lower scaling electronic structure methods such as Density Functional Theory (DFT) and MP2 including its spin-biased variants.

Heindel, Joseph↗
DOE OSTI2022

Finite Element Modeling of Diffusion in Fractured Porous Media by Using Hierarchical Material Properties

Abstract Fractured porous media challenge modeling approaches due to high computational costs and excessive mesh refinement imposed by the extreme scale variability of fractures and the heterogeneity of the surrounding porous rock. To overcome such difficulties, we utilize the hierarchical finite element method ( Hi ‐FEM) that has been developed previously to simulate the electrical potential distribution in complex geologic environments. The method employs the hierarchical basis functions in classical finite element analysis to enable representation of material properties on each dimensional component of a given 3D unstructured finite element, thereby inherently allowing for interactions at the boundary between fracture and a host rock. In this study, we extend its application to transient fluid flow and heat conduction in the Laplace domain. Time‐domain flow solutions are obtained by numerical inverse Laplace transform. We evaluate the accuracy of the method using different flow models and demonstrate its robustness for large‐scale, rock mass models featuring complex fracture networks. Moreover, for the computation of nodal Darcian velocity fields in fractured porous media where the fractures are represented as 2D features, a new approach that employs the Yeh's Galerkin model for both volume and facet elements is proposed. Results show that Hi ‐FEM can produce accurate flow solutions for fractured porous media without any need of coupling or transfer mechanism while still being computationally economical and numerically robust, even for large‐scale simulations.

Beskardes, G. D.↗
DOE OSTI2025

Multiscale Modeling Framework Using Element‐Based Galerkin Methods for Moist Atmospheric Limited‐Area Simulations

This paper presents a multiscale modeling framework (MMF) to model moist atmospheric limited-area weather. The MMF resolves large-scale convection using a coarse grid while simultaneously resolving local features through numerous fine local grids and coupling them seamlessly. Both large- and small-scale processes are modeled using the compressible Navier-Stokes equations within the Nonhydrostatic Unified Model of the Atmosphere (NUMA), and are discretized using a continuous element-based Galerkin method (spectral elements) with high-order basis functions. Consequently, the large-scale and small-scale models share the same dynamical core but have the flexibility to be adjusted individually. The proposed MMF method is tested in 2D and 3D idealized limited-area weather problems involving storm clouds produced by squall line and supercell simulations. Numerical results from the MMF showed enhanced representation of cloud processes compared to the coarse model.

Kang, Soonpil [Naval Postgraduate School, Monterey↗
DOE OSTI2021

Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon

The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code that is suitable for use in large-scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in shifts a previously established Pareto front for machine learning interatomic potentials toward faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A new approach for simulating inhomogeneous chemical kinetics

Abstract In this paper, inhomogeneous chemical kinetics are simulated by describing the concentrations of interacting chemical species by a linear expansion of basis functions in such a manner that the coupled reaction and diffusion processes are propagated through time efficiently by tailor-made numerical methods. The approach is illustrated through modelling $$\alpha$$ α - and $$\gamma$$ γ -radiolysis in thin layers of water and at their solid interfaces from the start of the chemical phase until equilibrium was established. The method’s efficiency is such that hundreds of such systems can be modelled in a few hours using a single core of a typical laptop, allowing the investigation of the effects of the underlying parameter space. Illustrative calculations showing the effects of changing dose-rate and water-layer thickness are presented. Other simulations are presented which show the approach’s capability to solve problems with spherical symmetry (an approximation to an isolated radiolytic spur), where the hollowing out of an initial Gaussian distribution is observed, in line with previous calculations. These illustrative simulations show the generality and the computational efficiency of this approach to solving reaction-diffusion problems. Furthermore, these example simulations illustrate the method’s suitability for simulating solid-fluid interfaces, which have received a lot of experimental attention in contrast to the lack of computational studies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

A new class of inhibitors of the AraC family virulence regulator

Vibrio cholerae is responsible for the diarrheal disease cholera that infects millions of people worldwide. While vaccines protecting against cholera exist, and oral rehydration therapy is an effective treatment method, the disease will remain a global health threat until long-term solutions such as improved sanitation and access to clean water become widely available. Because of this, there is a pressing need for potent therapeutics that can either mitigate cholera symptoms, or act prophylactically to prevent the virulent effects of a cholera infection. Here we report the design, synthesis, and characterization of a set of compounds that bind and inhibit ToxT, the transcription factor that directly regulates the two primary V. cholerae virulence factors. Using the folded structure of the monounsaturated fatty acid observed in the X-ray structure of ToxT as a template, we designed ten novel compounds that inhibit the virulence cascade to a greater degree than any known inhibitor. Our findings provide a structural and functional basis for the development of viable antivirulence therapeutics that combat cholera and, potentially, other forms of bacterial pathogenic disease.

Science & Technology - Other Topics↗
DOE OSTI2022

Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces

Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromouracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the $π_{2}^{*}$ resonance state and describes the formation of Br - anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.

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

A posteriori snapshot location for POD in optimal control of linear parabolic equations

In this paper we study the approximation of an optimal control problem for linear parabolic PDEs with model order reduction based on Proper Orthogonal Decomposition (POD-MOR). POD-MOR is a Galerkin approach where the basis functions are obtained upon information contained in time snapshots of the parabolic PDE related to given input data. In the present work we show that for POD-MOR in optimal control of parabolic equations it is important to have knowledge about the controlled system at the right time instances. We propose to determine the time instances (snapshot locations) by an a posteriori error control concept. The proposed method is based on a reformulation of the optimality system of the underlying optimal control problem as a second order in time and fourth order in space elliptic system which is approximated by a space-time finite element method. Finally, we present numerical tests to illustrate our approach and show the effectiveness of the method in comparison to existing approaches.

Mathematics↗
DOE OSTI2012

Trajectory-guided configuration interaction simulations of multidimensional quantum dynamics

We propose an approach to modelling multidimensional quantum systems which uses direct-dynamics trajectories to guide wavefunction propagation. First, trajectory simulations are used to generate a sample of dynamically relevant configurations on the potential energy surface (PES). Second, the sampled configurations are used to construct an n-mode representation of the PES using a greedy algorithm. Finally, the time-dependent Schroedinger equation is solved using a configuration interaction expansion of the wavefunction, with individual basis functions derived directly from the 1-mode contributions to the n-mode PES. This approach is successfully demonstrated by application to a 20-dimensional benchmark problem describing tunnelling in the presence of coupled degrees of freedom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Nonadiabatic anharmonic electron transfer

The effect of an inner sphere, local mode vibration on an electron transfer is modeled using the nonadiabatic transition probability (rate) expression together with both the anharmonic Morse and the harmonic oscillator potential. For an anharmonic inner sphere mode, a variational analysis uses harmonic oscillator basis functions to overcome the difficulties evaluating Morse-model Franck-Condon overlap factors. Individual matrix elements are computed with the use of new, fast, robust, and flexible recurrence relations. The analysis therefore readily addresses changes in frequency and/or displacement of oscillator minimums in the different electron transfer states. Direct summation of the individual Boltzmann weighted Franck-Condon contributions avoids the limitations inherent in the use of the familiar high-temperature, Gaussian form of the rate constant. The effect of harmonic versus anharmonic inner sphere modes on the electron transfer is readily seen, especially in the exoergic, inverted region. The behavior of the transition probability can also be displayed as a surface for all temperatures and values of the driving force/exoergicity {Delta}=-{Delta}G. The temperature insensitivity of the transfer rate is clearly seen when the exoergicity equals the collective reorganization energy ({Delta}={Lambda}{sub s}) along a maximum ln (w) vs. {Delta} ridge of the surface. The surface also reveals additional regions for {Delta} where ln (w) appears to be insensitive to temperature, or effectively activationless, for some kinds of inner sphere contributions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions

Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Asymptotic expansion of two-electron integrals and its application to Coulomb and exchange lattice sums in metallic, semimetallic, and nonmetallic crystals

A simple, easily implemented, accurate, and efficient approximation of long-range electron-electron-repulsion and electron-nucleus-attraction integrals is proposed. It replaces each product of two atomic-orbital (AO) basis functions of an electron by a point charge centered at the midpoint of the two AO's. The magnitude of the point charge is equal to the overlap integral of the two AO's. Each integral is then rapidly evaluated in the direct algorithm as a Coulomb interaction between two point charges. This scheme is implemented in ab initio Hartree–Fock crystalline orbital theory and tested for one-, two-, and three-dimensional solids of metallic, semimetallic, and nonmetallic electronic structures, in which the lattice sums of the direct Coulomb and/or exchange interactions are expected to be slowly convergent. It is shown that this approximation reduces operation and/or memory costs by up to an order of magnitude to achieve converged lattice sums, although the scaling (size dependence) of operation cost is unchanged. An improved criterion for truncating the exchange lattice sum is also proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Independent bases on the spatial wavefunction of four-identical-particle systems

We construct the independent bases on the spatial wavefunction of four-identical-particle systems classified under the rotational group SO(3) and the permutation group S{sub 4} with the usage of transformation coefficients that relate wavefunctions described in one set of internal coordinates with those in another. The basis functions for N⩽ 2 are presented in the explicit expressions based on the harmonic oscillator model. Such independent bases are supposed to play a key role in the construction of the wavefunctions of the five-quark states and the variation calculation of four-body systems. Our prescription avoids the spurious states and can be programmed for arbitrary N.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Reduced dimension rovibrational variational calculations of the S{sub 1} state of C{sub 2}H{sub 2}. I. Methodology and implementation

The bending and torsional degrees of freedom in S{sub 1} acetylene, C{sub 2}H{sub 2}, are subject to strong vibrational resonances and rovibrational interactions, which create complex vibrational polyad structures even at low energy. As the internal energy approaches that of the barrier to cis-trans isomerization, these energy level patterns undergo further large-scale reorganization that cannot be satisfactorily treated by traditional models tied to local minima of the potential energy surface for nuclear motion. Experimental spectra in the region near the cis-trans transition state have revealed these complicated new patterns. In order to understand near-barrier spectroscopic observations and to predict the detailed effects of cis-trans isomerization on the rovibrational energy level structure, we have performed reduced dimension rovibrational variational calculations of the S{sub 1} state. In this paper, we present the methodological details, several of which require special care. Our calculation uses a high accuracy ab initio potential surface and a fully symmetrized extended complete nuclear permutation inversion group theoretical treatment of a multivalued internal coordinate system that is appropriate for large amplitude bending and torsional motions. We also discuss the details of the rovibrational basis functions and their symmetrization, as well as the use of a constrained reduced dimension rovibrational kinetic energy operator.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗