Valence-programmable nanoparticle architectures
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99 GENERAL AND MISCELLANEOUS↗
SEARCH · Engineering Papers
Results for “cluster structure”
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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Geographic_Distribution_of_Populus_trichocarpa_Genotypes_by_DBSCAN_Cluster
Aninteractive mapshowingPopulus trichocarpaGWAS sub-population structure identified by DBSCAN clustering, which were derived from a UMAP projection of the top 8 PCs of LD-pruned pangenome SNP data. Geographic origins are searchable by genotype or river system using the search bar.
09 BIOMASS FUELS↗
Long-range three-dimensional magnetic structures of the spin S =1 hexamer cluster fedotovite-like A 2 Cu 3 O ( SO 4 ) 3 ( A 2 = K 2 , NaK, Na 2 ): A neutron diffraction study
The crystal and magnetic structures of the spin S = 1 hexamer cluster fedotovite-like A 2 Cu 3 O(SO 4 ) 3 (A 2 = K 2 , NaK, Na 2 ) were studied by neutron powder diffraction at temperatures 1.6–290 K. The crystal structures in all compounds are well refined in the monoclinic space group C2/c. The basic magnetic units of the compounds are copper hexamers, which are coupled by weak superexchange interactions giving rise to three-dimensional long-range magnetic order below 3.0 < T N < 4.7 K. We have found that for A 2 = K 2 and NaK the propagation vector of the magnetic structure is k = [0,0,0], and the coupling of the Cu hexamers is ferromagnetic (FM) along the ab diagonal and antiferromagnetic along the bc diagonal. In contrast, for A = Na the propagation vector is k = [0,1,0], and the Cu hexamers are coupled antiferromagnetically (AFM) along the ab diagonal. Further, the hexamers are formed by three Cu pairs arranged along the b axis. The calculated spin expectation values $\langle s \rangle$ for the simplest symmetric spin Hamiltonian (obtained from inelastic neutron spectroscopy) of the isolated hexamers in the mean field amounted to $\langle s \rangle$ = 3/8 for the side spins Cu1 and Cu2 and $\langle s \rangle$ = 1/4 for Cu3 in the middle. The Cu spins are FM coupled in pairs and AFM between neighboring pairs. The experimental magnetic moments of the Cu 2+ ions turn out to be not completely collinear due to spin frustrations within the weak interhexamer interactions. The sizes of magnetic moments of Cu in the hexamers determined from the diffraction data are in fair agreement with the calculated values.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Active Learning A Neural Network Model For Gold Clusters & Bulk From Sparse First Principles Training Data
Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Given the high computational cost of first-principles calculations, molecular modeling and atomistic simulations such as molecular dynamics (MD) has proven to be an important complementary tool to aid this understanding. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities (similar to 10 4 or greater) of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. A highly desirable goal is minimize the number of training data, especially if the underlying reference model is first-principles based and hence expensive. In this work, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (similar to 1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with similar to 500 total reference calculations. Using an extensive DFT test set of similar to 1100 configurations, we show that our AL-NN is able to accurately predict both the DFT energies and the forces for clusters of a myriad of different sizes. Our NN predictions are within 30 meV/atom and 40 meV/angstrom of the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments. We finally show that our AL-NN model also captures bulk properties reasonably well, even though they were not included in the training data.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
PDBspheres: a method for finding 3D similarities in local regions in proteins
Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.
59 BASIC BIOLOGICAL SCIENCES↗
Structure and Stability of the Ionic Liquid Clusters [EMIM]n[BF4]n+1- (n = 1 – 9): Implications for Electrochemical Separations
Precise functionalization of electrodes with size-selected ionic liquid (IL) clusters may improve the application of ILs in electrochemical separations. Herein, we report our combined experimental and theoretical investigation of the IL clusters [EMIM]????[BF4]????+1- (n = 1 – 9) and demonstrate their selectivity and efficiency towards targeted adsorption of molecules from solution. The structures and energies of the IL clusters, predicted with global optimization, agree with and help interpret the ion abundances and stabilities measured by high mass resolution electrospray ionization mass spectrometry and collision induced dissociation experiments. The [EMIM][BF4]2- cluster, which was identified as the most stable IL cluster, was selectively soft landed onto a working electrode. Electrochemical impedance spectroscopy revealed a lower charge transfer resistance on the soft-landed electrode containing [EMIM] [BF_4 ]_2^- compared to an electrode prepared by drop casting of IL solution, which contains the full range of IL clusters. Our findings indicate that specific IL clusters may be used to increase the efficiency of electrochemical separations by lowering the overpotentials involved.
Zhang, Jun↗
The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the growth rate of structure from the small-scale clustering of the luminous red galaxy sample
ABSTRACT We measure the small-scale clustering of the Data Release 16 extended Baryon Oscillation Spectroscopic Survey Luminous Red Galaxy sample, corrected for fibre-collisions using Pairwise Inverse Probability weights, which give unbiased clustering measurements on all scales. We fit to the monopole and quadrupole moments and to the projected correlation function over the separation range $7-60\, h^{-1}{\rm Mpc}$ with a model based on the aemulus cosmological emulator to measure the growth rate of cosmic structure, parametrized by fσ8. We obtain a measurement of fσ8(z = 0.737) = 0.408 ± 0.038, which is 1.4σ lower than the value expected from 2018 Planck data for a flat ΛCDM model, and is more consistent with recent weak-lensing measurements. The level of precision achieved is 1.7 times better than more standard measurements made using only the large-scale modes of the same sample. We also fit to the data using the full range of scales $0.1\text{--}60\, h^{-1}{\rm Mpc}$ modelled by the aemulus cosmological emulator and find a 4.5σ tension in the amplitude of the halo velocity field with the Planck + ΛCDM model, driven by a mismatch on the non-linear scales. This may not be cosmological in origin, and could be due to a breakdown in the Halo Occupation Distribution model used in the emulator. Finally, we perform a robust analysis of possible sources of systematics, including the effects of redshift uncertainty and incompleteness due to target selection that were not included in previous analyses fitting to clustering measurements on small scales.
79 ASTRONOMY AND ASTROPHYSICS↗
3C 323.1 - A QSO in a rich cluster of galaxies.
The redshift and structural data on the compact cluster Zw Cl 1545.1+2104 have been determined from deep plates of the cluster region and from spectral scans of the central galaxy in the cluster. The cluster is of richness 1 on Abell's (1958) scale, and the redshift of its central galaxy agrees well with that of the quasar 3C 323.1 which lies at a projected distance of 6.5 sec from the center of the cluster. The data indicate that the quasar is a member of the cluster as opposed to the observed trend.
Oemler, A., Jr.↗
Adaptive Conformer Sampling for Property Prediction Using the Conductor-like Screening Model for Real Solvents
The valorization of lignocellulose-derived bioproducts requires effective separation from excessive water. Liquid–liquid extraction is a promising low-energy separation technology, but effective extraction requires solvent selection based on the thermodynamic properties of the bioproduct and solvent components. We propose a computational framework for predicting such properties by developing an adaptive conformer selection approach for use with COSMO-RS (conductor-like screening model for real solvents) calculations. In this framework, molecular dynamics simulations are used to generate many molecular structures (conformers) at representative temperatures in varying solvent environments. Conformers are then clustered based on structural metrics in a low-dimensional space and selected using a mixed-integer quadratic programming problem to iteratively insert a sampled conformer. At each iteration, we determine bioproduct properties using COSMO-RS. Here, we demonstrate the capability of the proposed framework on representative bioproducts to show convergence of the adaptive sampling toward experimentally measured properties with fewer calculations than required by random conformer sampling, enabling the improved screening of solvent systems for liquid-phase separation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Study of Clusters of Galaxies and Large Scale Structures
Many research projects have been initiated and completed under support of this program. The results are summarized below. The work on the ROSAT Deep Survey has been successfully completed. A number of interesting results have been established within this joint MPE, Cal Tech, JHU, ST ScI, ESO collaboration. First, a very large fraction, 70-80 percent, of the X-ray background has been directly resolved into point sources. We have derived a new log N-log S for X-ray sources and have measured a source density of 970 sources per square degree at a limiting flux level. Care was taken in these studies to accurately model and measure the effects of sources confusion. This was possible because of our observing strategy which included both deep PSPC and HRI observations. No evidence of a population of narrow emission line galaxies has been established but some evidence for the evolution of low luminosity AGN (Seyfert galaxies) has been reported. The work on the ROSAT All Sky Survey Northern Cluster Survey has been substantially concluded but the publication of the list has been held up by the need to analyze newly re-calibrated data. This should result in publication over the next year. During the past year we have submitted a paper to the Astrophysical Journal which utilized a sample of clusters originally selected from the ROSAT All-sky survey at redshifts greater than 0.3. This sample was studied with ASCA to determine temperature and luminosity.
Source record↗
Formation and transformation of iron oxy-hydroxide precursor clusters to ferrihydrite
Iron (Fe) oxy-hydroxide minerals such as ferrihydrite (Fh) are ubiquitous in Earth-surface environments and important in biogeochemical element cycling. Recent research has suggested that their formation is preceded by the precipitation of ultrasmall (~1 nm) Keggin-like Fe oxy-hydroxide clusters. However, relatively little is understood about the structure of the precursor clusters and the impacts of pH and time on their growth and transformation to more stable phases. Here, we used a new method that involves mixed flow reactors (MFR) to synthesize these Fe oxy-hydroxide precursor clusters at pH 1.0, 1.5, 2.5, and 4.5. In situ and ex situ synchrotron scattering measurements and laboratory small-angle X-ray scattering (SAXS) were used to study the structure and size of Fe oxy-hydroxide clusters and their transformation products, respectively. Results show that with increasing pH, the particle size and structural order of samples increase, forming solids that resemble 2-line Fh at pH 4.5. The experimental data were compared with X-ray pair distribution functions (PDF) calculated for a range of Fe(III) oxyhydroxide clusters, including Fe 13 Keggin isomers computed previously using density functional theory (DFT), which yielded at best only partial agreement at short range (<5 Å). Aging of the clusters synthesized at pH 1.5 and 2.5 results in growth and transformation via Ostwald ripening to mixtures of goethite (Gt) and lepidocrocite (Lp). This process was inhibited by immediately reacting the early-formed clusters with phosphate (PO 4 3– ), suggesting that oxyanion surface complexes can stabilize the initial clusters by preventing growth and crystallization to more stable phases.
58 GEOSCIENCES↗
Fine-Scale Filamentary Structure in Coronal Streamers
Doppler scintillation measurements of a coronal streamer lasting several solar rotations have been conducted by Ulysses in 1991 over a heliocentric distance range of 14-77 R(sub 0). By showing that the solar corona is filamentary, and that Doppler frequency is the radio counterpart of white-light eclipse pictures processed to enhance spatial gradients, it is demonstrated that Doppler scintillation measurements provide the high spatial resolution that has long eluded white-light coronagraph measurements. The region of enhanced scintillation, spanning an angular extent of 1.8 deg in heliographic longitude, coincides with the radially expanding streamer stalk and represents filamentary structure with scale sizes at least as small as 340 km (0.5 sec) when extrapolated to the Sun. Within the stalk of the streamer, the fine-scale structure corresponding to scale sizes in the range of 20-340 km at the Sun and associated with closed magnetic fields amounts to a few percent of the mean density, while outside the stalk, the fine-scale structure associated with open fields is an order of magnitude lower. Clustering of filamentary structure that takes place within the stalk of the streamer is suggestive of multiple current sheets. Comparison with ISEE 3 in situ plasma measurements shows that significant evolution resulting from dynamic interaction with increasing heliocentric distance takes place by the time streamers reach Earth orbit.
Woo, Richard↗
Numerical models of jet disruption in cluster cooling flows
We present a coherent picture for the formation of the observed diverse radio morphological structures in dominant cluster galaxies based on the jet Mach number. Realistic, supersonic, steady-state cooling flow atmospheres are evolved numerically and then used as the ambient medium through which jets of various properties are propagated. Low Mach number jets effectively stagnate due to the ram pressure of the cooling flow atmosphere while medium Mach number jets become unstable and disrupt in the cooling flow to form amorphous structures. High Mach number jets manage to avoid disruption and are able to propagate through the cooling flow.
Loken, Chris↗
Frataxin Traps Low Abundance Quaternary Structure to Stimulate Human Fe–S Cluster Biosynthesis
Not provided.
Biochemistry & Molecular Biology↗
Crystal Structure of the [4Fe?4S] Cluster-Containing Adenosine-5;#8242;-phosphosulfate Reductase fro
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Feliciano, Patricia R.↗
Theoretical approaches to metal chemistry
Theoretical calculations on metals ranging from very accurate ab initio studies of diatomic and triatomic systems to model studies of larger clusters are presented. Recent improvements in the representation of one-particle and n-particle spaces have made possible the prediction that Al2 has a 3Pi(u) ground state, even though the 3Sigma(-)g state lies within 200/cm. Results suggest that cluster geometry varies dramatically with cluster size, and that rather large clusters are required before the bulk structure becomes optimal. Al cluster studies show that three-body terms are needed for quantitative agreement with ab initio calculations.
Bauschlicher, Charles W.↗
Modified Newtonian dynamics and the Coma cluster
The consistency of Milgrom's theory of modified Newtonian dynamics is checked against optical and X-ray data for the Coma cluster of galaxies. It is found that viable models for the cluster containing no dark matter can be constructed. They require an extensive gaseous atmosphere through which galaxies move on near-radial orbits. The gas temperature is predicted to have a shallow minimum near the cluster center; this structure may conflict with the best X-ray spectra of the cluster.
The, Lih Sin↗