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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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural and Dynamical Design Principles for Iron-Sulfur Clusters in Sequence Defined Polymers

This integrated synthetic and computational effort uses sequence defined polymers such as peptoids, and triazines, capable of mimicking a flexible protein environment to control the positioning of side chains around redox cofactors. This strategy will allow modulation of redox properties through both direct and indirect mechanisms. To this end the aim is defined to test the underlying hypothesis: that principles and critical functionalities governing the binding and tuning of naturally occurring electron carrier co-factors can be identified and used to predictably design and synthesize maquettes based on non-natural polymers resulting in new modular biomimetic scaffolds for Electron Transfer Materials. This will be achieved through design and synthesis of ligands that can stabilize iron-sulfur clusters and tune the redox potential based on sequence.

36 MATERIALS SCIENCE↗
DOE OSTI2015

CHANDRA and XMM-NEWTON observations of the bimodal PLANCK SZ -detected clustered CKG345.40-39.34 (A3716) with high and low entropy subcluster cores

Here, we present results from Chandra, XMM-Newton, and ROSAT observations of the Planck SZ-detected cluster A3716 (PLCKG345.40-39.34-G345). We show that G345 is, in fact, two subclusters separated on the sky by 400 kpc. We measure the subclusters' gas temperatures (~2–3 keV), total (~1–2 × 10 14 ${{M}_{\odot }}$) and gas (~1–2 × 10 13 ${{M}_{\odot }}$) masses, gas mass fraction within r500, entropy profiles, and X-ray luminosities (~10 43 erg s -1 ). Using the gas density and temperature profiles for both subclusters, we show that there is good (0.8σ) agreement between the expected Sunyaev–Zel'dovich signal predicted from the X-ray data and that measured from the Planck mission, and better agreement within 0.6σ when we re-computed the Planck value assuming a two component cluster model, with relative amplitudes fixed based on the X-ray data. Dynamical analysis shows that the two galaxy subclusters are very likely ($\gt 97\%$ probability) gravitationally bound, and in the most likely scenario, the subclusters will undergo core passage in 500 ± 200 Myr. The northern subcluster is centrally peaked and has a low entropy core, while the southern subcluster has a high central entropy. Finally, the high central entropy in the southern subcluster can be explained either by the mergers of several groups, as suggested by the presence of five giant ellipticals or by active galactic nucleus energy injection, as suggested by the presence of a strong radio source in one of its massive elliptical galaxies, or by a combination of both processes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Hedgehog bases for A n cluster polylogarithms and an application to six-point amplitudes

Multi-loop scattering amplitudes in N=4 Yang-Mills theory possess cluster algebra structure. In order to develop a computational framework which exploits this connection, we show how to construct bases of Goncharov polylogarithm functions, at any weight, whose symbol alphabet consists of cluster coordinates on the A n cluster algebra. As a result, using such a basis we present a new expression for the 2-loop 6-particle NMHV amplitude which makes some of its cluster structure manifest.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

New voyages to explore the natural product galaxy

Abstract Natural products are a large family of diverse and complex chemical molecules that have roles in both primary and secondary metabolism, and over 210,000 natural products have been described. Secondary metabolite natural products are of high commercial and societal value with therapeutic uses as antibiotics, antifungals, antitumor and antiparasitic products and in agriculture as products for crop protection and animal health. There is a resurgence of activity in exploring natural products for a wide range of applications, due to not only increasing antibiotic resistance, but the advent of next-generation genome sequencing and new technologies to interrogate and investigate natural product biosynthesis. Genome mining has revealed a previously undiscovered richness of biosynthetic potential in novel biosynthetic gene clusters for natural products. Complementing these computational processes are new experimental platforms that are being developed and deployed to access new natural products.

Mouncey, Nigel J.↗
DOE OSTI2016

Structure-based design of broadly protective group a streptococcal M protein-based vaccines

Here, a major obstacle to the development of broadly protective M protein-based group A streptococcal (GAS) vaccines is the variability within the N-terminal epitopes that evoke potent bactericidal antibodies. The concept of M type-specific protective immune responses has recently been challenged based on the observation that multivalent M protein vaccines elicited cross-reactive bactericidal antibodies against a number of non-vaccine M types of GAS. Additionally, a new “cluster-based” typing system of 175 M proteins identified a limited number of clusters containing closely related M proteins. In the current study, we used the emm cluster typing system, in combination with computational structure-based peptide modeling, as a novel approach to the design of potentially broadly protective M protein-based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High-Precision Calculation of Nanoparticle (Nanocrystal) Potentials of Mean Force and Internal Energies

Thermodynamic stability assessment of nanocrystal systems requires precise free energy calculations. This study highlights the importance of meticulous control over various factors, including the thermostat, time step, potential cutoff, initial configuration, sampling method, and overall simulation duration. Free energy computations in dry (solvent-free) systems are on the order of several hundred $k_BT$ but can be obtained with consistent accuracy. However, calculation of internal energies becomes challenging, as they are typically much larger in magnitude than free energies and exhibit significant noise and reduced reliability. To address this limitation, we propose a new internal energy estimate that drastically reduces the noise. Here, we also present formulas that enable the optimization of the parameters of the harmonic bias potential for optimal convergence. Finally, we discuss the implications of these findings for the computation of free energies in nanocrystal clusters and superlattices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Classical Preoptimization Approach for ADAPT-VQE: Maximizing the Potential of High-Performance Computing Resources to Improve Quantum Simulation of Chemical Applications

The ADAPT-VQE algorithm is a promising method for generating a compact ansatz based on derivatives of the underlying cost function, and it yields accurate predictions of electronic energies for molecules. In this work, we report the implementation and performance of ADAPT-VQE with our recently developed sparse wave function circuit solver (SWCS) in terms of accuracy and efficiency for molecular systems with up to 52 spin orbitals. The SWCS can be tuned to balance computational cost and accuracy, which extends the application of ADAPT-VQE for molecular electronic structure calculations to larger basis sets and a larger number of qubits. Using this tunable feature of the SWCS, we propose an alternative optimization procedure for ADAPT-VQE to reduce the computational cost of the optimization. Furthermore, by preoptimizing a quantum simulation with a parametrized ansatz generated with ADAPT-VQE/SWCS, we aim to utilize the power of classical high-performance computing in order to minimize the work required on noisy intermediate-scale quantum hardware, which offers a promising path toward demonstrating quantum advantage for chemical applications.

ADAPT-VQE↗
DOE OSTI2018

A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT)

Extended symmetry-adapted perturbation theory (XSAPT), in conjunction with empirical “+aiD” potentials fit to ab initio dispersion data, is a low-scaling approach to compute intermolecular interaction energies in noncovalent clusters. One shortcoming is that the aiD atom–atom dispersion potentials are independent of the chemical environment of the atoms in question and therefore neglect nonadditive dispersion effects. These can be significant in large systems, so to account for them we test a simple correction to XSAPT(KS)+aiD, where “KS” indicates the use of Kohn–Sham orbitals. This correction, which can be evaluated at fourth-order cost using double-ζ basis sets, is based on comparing second-order SAPT dispersion with and without a self-consistent charge embedding for the monomer wave functions. The correction amounts to ~1.4 kcal/mol in (H 2 O) 6 but ~5.5 kcal/mol in (H 2 O) 20 . With the nonadditive dispersion correction, XSAPT(KS)+aiD affords errors of ~1 kcal/mol for isomers of F–(H 2 O) 10 and (H 2 O) 20 , where the benchmarks are complete-basis CCSD(T) energies, as well as for ion–water clusters X(H 2 O)n where n ≤ 6 and X = F – , Cl – , SO 4 2– , Li + , Na + , or K + . We also test the MP2 method and a variety of density-functional methods that have been specifically recommended for noncovalent interactions. Among the latter, only ωB97X-V and ωB97M-V can be recommended for ion–water clusters, as mean errors for other popular approaches (including ωB97X-D3 and several Minnesota functionals) exceed 1 kcal/mol. Lastly, we examine clathrate-hydrate host/guest complexes whose mixture of hydrogen bonding and dispersion make them challenging tests for noncovalent quantum chemistry. Although the B97-D2 functional performs best for clathrate hydrates and has been previously recommended in other studies of these inclusion complexes, its performance for other systems examined here is quite poor. We are unable to find a functional whose accuracy is ≲1 kcal/mol accuracy for both clathrate hydrates and ion–water clusters. However, the XSAPT(KS)+aiD method with the nonadditive dispersion correction can achieve this, with a mean error for the clathrate hydrates of 0.3 kcal/mol.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Capturing Surface Coverage Effects in Heterogeneous Catalysis

Adsorbate–adsorbate lateral interactions at relevant surface coverages have a significant effect on chemical kinetics, thereby influencing the activity of a heterogeneous catalyst. Coverage-dependent kinetic and thermodynamic parameters therefore must be included in studies of such complex systems to properly predict the turnover frequencies and kinetic trends. Thus, it becomes extremely important to accurately capture the strength of lateral interactions between neighboring species under realistic reaction conditions. In this Perspective, we discuss the various existing computational and experimental methods for determining adspecies coverage and configurational effects. The choice of the tools and methods employed in such studies depends on factors such as time, length scales, computational cost, the presence of solvents, and reaction conditions. The applications of each method and the respective challenges are also discussed here. As a result, we discuss the recent developments and future of the state-of-the-art for inclusion of surface coverage and configuration into a holistic picture for accurate predictions of catalytic behavior.

09 BIOMASS FUELS↗
DOE OSTI2023

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).

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

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

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

The first potential energy surfaces for the C{sub 6}H{sup −}–H{sub 2} and C{sub 6}H{sup −}–He collisional systems and their corresponding inelastic cross sections

Molecular anions have recently been detected in the interstellar and circumstellar media. Accurate modeling of their abundance requires calculations of collisional data with the most abundant species that are usually He atoms and H{sub 2} molecules. In this paper, we focus on the collisional excitation of the first observed molecular anion, C{sub 6}H{sup −}, by He and H{sub 2}. Theoretical calculations of collisional cross sections rely generally on ab initio interaction potential energy surfaces (PESs). Hence, we present here the first PESs for the C{sub 6}H{sup −}–H{sub 2} and C{sub 6}H{sup −}–He van der Waals systems. The ab initio energy data for the surfaces were computed at the explicitly correlated coupled cluster with single, double, and scaled perturbative triple excitations level of theory. The method of interpolating moving least squares was used to construct 4D and 2D analytical PESs from these data. Both surfaces are characterized by deep wells and large anisotropies. Analytical models of the PESs were used in scattering calculations to obtain cross sections for low-lying rotational transitions. As could have been anticipated, important differences exist between the He and H{sub 2} cross sections. Conversely, no significant differences exist between the collisions of C{sub 6}H{sup −} with the two species of H{sub 2} (para- and ortho-H{sub 2}). We expect that these new data will help in accurately determining the abundance of the C{sub 6}H{sup −} anions in space.

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

Asynchronous quadratic control for constrained hidden markov jump linear systems with incomplete MTPM and MOCPM

Abstract This paper investigates the quadratic optimal control problem for constrained Markov jump linear systems with incomplete mode transition probability matrix (MTPM). Considering original system mode is not accessible, observed mode is utilized for asynchronous controller design where mode observation conditional probability matrix (MOCPM), which characterizes the emission between original modes and observed modes is assumed to be partially known. An LMI optimization problem is formulated for such constrained hidden Markov jump linear systems with incomplete MTPM and MOCPM. Based on this, a feasible state-feedback controller can be designed with the application of free-connection weighting matrix method. The desired controller, dependent on observed mode, is an asynchronous one which can minimize the upper bound of quadratic cost and satisfy restrictions on system states and control variables. Furthermore, clustering observation where observed modes recast into several clusters, is explored for simplifying the computational complexity. Numerical examples are provided to illustrate the validity.

Zhu, Jin↗
DOE OSTI2021

Inelastic rate coefficients for collisions of C 4 H - with H 2

Carbon-chain anions were recently detected in the interstellar medium. These very reactive species are used as tracers of the physical and chemical conditions in a variety of astrophysical environments. However, the local thermodynamic equilibrium conditions are generally not fulfilled in these environments. Therefore, collisional as well as radiative rates are needed to accurately model the observed emission lines. We determine in this work the state-to-state rate coefficients of C 4 H- in collision with both ortho- and para-H 2 . A new ab initio 4D potential energy surface was computed using explicitly correlated coupled-cluster procedures. This surface was then employed to determine rotational excitation and de-excitation cross-sections and rate coefficients for the first 21 rotational levels (up to rotational level j 1 = 20) using the close-coupling method, while the coupled-state approximation was used to extend the calculations up to j 1 = 30. State-to-state rate coefficients were obtained for the temperature range 2–100K. The differences between the ortho- and para-H 2 rate coefficients are found to be small.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Two-particle correlation functions in cluster perturbation theory: Hubbard spin susceptibilities

Cluster perturbation theory (CPT) is a computationally economic method commonly used to estimate the momentum- and energy-resolved single-particle Green's function. It has been used extensively in direct comparisons with experiments that effectively measure the single-particle Green's function, e.g., angle-resolved photoemission spectroscopy. However, many experimental observables are given by two-particle correlation functions. CPT can be extended to compute two-particle correlation functions by approximately solving the Bethe-Salpeter equation. We implement this method and focus on the transverse spin susceptibility, measurable via inelastic neutron scattering or with optical probes of atomic gases in optical lattices. Finally, we benchmark the method with the one-dimensional Fermi-Hubbard model by comparing with known results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Efficient Ab initio Modeling of Random Multicomponent Alloys

Here, we present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multi-component alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we also demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high entropy alloy chemistries. Furthermore, the SSOS method developed here can be broadly useful for the rapid computational design of multi-component materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

36 MATERIALS SCIENCE↗