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At least 721 records · Page 40

Deducing subnanometer cluster size and shape distributions of heterogeneous supported catalysts

Abstract Infrared (IR) spectra of adsorbate vibrational modes are sensitive to adsorbate/metal interactions, accurate, and easily obtainable in-situ or operando. While they are the gold standards for characterizing single-crystals and large nanoparticles, analogous spectra for highly dispersed heterogeneous catalysts consisting of single-atoms and ultra-small clusters are lacking. Here, we combine data-based approaches with physics-driven surrogate models to generate synthetic IR spectra from first-principles. We bypass the vast combinatorial space of clusters by determining viable, low-energy structures using machine-learned Hamiltonians, genetic algorithm optimization, and grand canonical Monte Carlo calculations. We obtain first-principles vibrations on this tractable ensemble and generate single-cluster primary spectra analogous to pure component gas-phase IR spectra. With such spectra as standards, we predict cluster size distributions from computational and experimental data, demonstrated in the case of CO adsorption on Pd/CeO 2 (111) catalysts, and quantify uncertainty using Bayesian Inference. We discuss extensions for characterizing complex materials towards closing the materials gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Water confinement in small polycyclic aromatic hydrocarbons

The confinement of water molecules is vital in fields from biology to nanotechnology. The conditions allowing confinement in small finite polycyclic aromatic hydrocarbons (PAHs) are unclear, yet are crucial for understanding confinement in larger systems. Here, we report a computational study of water cluster confinement within PAHs dimers. Our results serve as a model for larger carbon allotropes and for understanding molecular interactions in confined systems. We identified size and structural motifs allowing confinement and demonstrated the motifs in various PAHs systems. Here we show that optimal OH∙∙∙π interactions between water clusters and the PAH dimer permit optimal confinement to occur. However, the lack of such interactions leads to the formation of CH∙∙∙O interactions, resulting in less ideal confinement. Confinement of layered clusters is also possible, provided that the optimal OH∙∙∙π interactions are conserved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laboratory study of isocyanic acid ions: Rotational spectroscopy of NCO{sup −}, H{sub 2}NCO{sup +}, and HNCOH{sup +}

We report detection of protonated isocyanic acid in two isomeric forms, H{sub 2}NCO{sup +} and HNCOH{sup +}, by high-resolution spectroscopy. The two ions were first observed at centimeter wavelengths by Fourier Transform (FT) microwave spectroscopy, in a discharge through HNCO heavily diluted in hydrogen in the throat of a supersonic nozzle. Spectroscopic constants derived from the two lowest rotational transitions of both isomers agree very well with those derived from theoretical structures computed at the coupled cluster level of theory. In the same molecular beam, the fundamental rotational transition of NCO{sup −} was observed with well-resolved nitrogen quadrupole hyperfine structure. Detection of NCO{sup −} and H{sub 2}NCO{sup +} in our beam was subsequently confirmed by observation of several millimeter-wave transitions in a low pressure discharge through cyanogen and water. The spectroscopic constants of NCO{sup −} obtained earlier by infrared laser spectroscopy are in good agreement with the highly accurate constants derived here. Owing to the high abundance of HNCO in many galactic molecular sources, both ions are excellent candidates for astronomical detection in the radio band.

74 ATOMIC AND MOLECULAR PHYSICS↗

Merging ab initio theory and few-body approach for (d, p) reactions

A framework for A(d, p)B reactions is introduced by merging the microscopic approach to computing the properties of the nucleon-target systems and the three-body n + p + A reaction formalism, thus providing a consistent link between the reaction cross sections and the underlying microscopic structure. In this first step toward a full microscopic description, we focus on the inclusion of the neutron-target microscopic properties. The properties of the neutron-target subsystem are encapsulated in the Green's function which is computed with the coupled Cluster theory using a chiral nucleon-nucleon and three-nucleon interactions. Subsequently, this many-body information is introduced in the few-body Green's Function Transfer approach to (d, p) reactions. Our benchmarks on stable targets 40,48 Ca show an excellent agreement with the data. We then proceed to make specific predictions for (d, p) on neutron rich 52,54 Ca isotopes. These predictions are directly relevant to testing the new magic numbers N = 32, 34 and are expected to be feasible in the first campaign of the projected FRIB facility.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Collisional excitation of CH 2 rotational/fine-structure levels by helium

Accurate determination of the abundance of CH 2 in interstellar media relies on both radiative and collisional rate coefficients. Here, we investigate here the rotational/fine-structure excitation of CH 2 induced by collisions with He. We employ a recoupling technique to generate fine-structure-resolved cross-sections and rate coefficients from close coupling spin-free scattering calculations. The calculations are based on a recent, high-accuracy CH 2 –He potential energy surface computed at the coupled clusters level of theory. The collisional cross-section calculations are performed for all fine-structure transitions among the first 22 and 24 energy levels of ortho- and para-CH 2 , respectively, and for temperatures up to 300 K. As a first application, we simulate the excitation of CH 2 in typical molecular clouds. The excitation temperatures of the CH 2 lines are found to be small at typical densities of molecular clouds, showing that the non-local thermodynamic equilibrium approach has to be used to analyse interstellar spectra. We also found that the fine-structure lines connected with the 404 – 313 and 505 – 414 rotational transitions show possible maser emissions so that they can be easily seen in emission. In conclusion, these calculations show that CH 2 may have to be detected mainly through absorption spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coherent elastic neutrino-nucleus scattering on Ar 40 from first principles

Coherent elastic neutrino scattering on the 40 Ar nucleus is computed with coupled-cluster theory based on nuclear Hamiltonians inspired by effective field theories of quantum chromodynamics. Our approach is validated by calculating the charge form factor and comparing it to data from electron scattering. We make predictions for the weak form factor, the neutron radius, and the neutron skin and estimate systematic uncertainties. The neutron-skin thickness of 40 Ar is consistent with results from density-functional theory. Precision measurements from coherent elastic neutrino-nucleus scattering could potentially be used to extract these observables and help to constrain nuclear models.

39 ≤ A ≤ 58↗

Exactness of the normal-ordered two-body truncation of three-nucleon forces

Reference-state-based many-body methods start from Hamiltonians that are normal ordered with respect to the reference state. In low-energy nuclear physics applications, normal-ordered Hamiltonians consisting of two- and three-nucleon forces are usually truncated at the two-body rank with residual three-nucleon operators being discarded. Benchmark computations have shown that this truncation is accurate, but we lack an understanding about why it works. Here, we show that the normal-ordered two-body truncation is exact for zero-range three-body forces when nuclei are computed using the coupled cluster with singles and doubles method. As the nuclear three-nucleon force is short ranged and a three-body contact is a leading term in effective field theories of quantum chromodynamics, our result provides an analytical basis for the popular normal-ordered two-body approximation.

Rothman, Maxwell [Univ. of Tennessee, Knoxville, T↗

A Visual Analytics Paradigm Enabling Trillion-Edge Graph Exploration

We present a visual analytics paradigm and a system prototype for exploring web-scale graphs. A web-scale graph is described as a graph with ~one trillion edges and ~50 billion vertices. While there is an aggressive R&D effort in processing and exploring web-scale graphs among internet vendors such as Facebook and Google, visualizing a graph of that scale still remains an underexplored R&D area. The paper describes a nontraditional peek-and-filter strategy that facilitates the exploration of a graph database of unprecedented size for visualization and analytics. We demonstrate that our system prototype can 1) preprocess a graph with ~25 billion edges in less than two hours and 2) support database query and visualization on the processed graph database afterward. Based on our computational performance results, we argue that we most likely will achieve the one trillion edge mark (a computational performance improvement of 40 times) for graph visual analytics in the near future.

graph visualization↗

Joint Estimation of Topology and Injection Statistics in Distribution Grids with Missing Nodes

Optimal operation of distribution grid resources relies on accurate estimation of its state and topology. Practical estimation of such quantities is complicated by the limited presence of real-time meters. This article discusses a theoretical framework to jointly estimate the operational topology and statistics of injections in radial distribution grids under limited availability of nodal voltage measurements. In particular, we show that our proposed algorithms are able to provably learn the exact grid topology and injection statistics at all unobserved nodes as long as they are not adjacent. The algorithm design is based on novel ordered trends in voltage magnitude fluctuations at node groups, that are independently of interest for radial physical flow networks. The complexity of the designed algorithms is theoretically analyzed and their performance is validated using both linearized and nonlinear ac power flow samples in test distribution grids.

97 MATHEMATICS AND COMPUTING↗

SU-F-R-08: Can Normalization of Brain MRI Texture Features Reduce Scanner-Dependent Effects in Unsupervised Machine Learning?

Purpose: To reduce differences in features calculated from MRI brain scans acquired at different field strengths with or without Gadolinium contrast. Methods: Brain scans were processed for 111 epilepsy patients to extract hippocampus and thalamus features. Scans were acquired on 1.5 T scanners with Gadolinium contrast (group A), 1.5T scanners without Gd (group B), and 3.0 T scanners without Gd (group C). A total of 72 features were extracted. Features were extracted from original scans and from scans where the image pixel values were rescaled to the mean of the hippocampi and thalami values. For each data set, cluster analysis was performed on the raw feature set and for feature sets with normalization (conversion to Z scores). Two methods of normalization were used: The first was over all values of a given feature, and the second by normalizing within the patient group membership. The clustering software was configured to produce 3 clusters. Group fractions in each cluster were calculated. Results: For features calculated from both the non-rescaled and rescaled data, cluster membership was identical for both the non-normalized and normalized data sets. Cluster 1 was comprised entirely of Group A data, Cluster 2 contained data from all three groups, and Cluster 3 contained data from only groups 1 and 2. For the categorically normalized data sets there was a more uniform distribution of group data in the three Clusters. A less pronounced effect was seen in the rescaled image data features. Conclusion: Image Rescaling and feature renormalization can have a significant effect on the results of clustering analysis. These effects are also likely to influence the results of supervised machine learning algorithms. It may be possible to partly remove the influence of scanner field strength and the presence of Gadolinium based contrast in feature extraction for radiomics applications.

60 APPLIED LIFE SCIENCES↗

Virtual Flow Simulator

Virtual Flow Simulator (VFS) is a state-of-the-art computational fluid mechanics (CFD) package that is capable of simulating multi-physics/multi-phase flows with the most advanced turbulence models (RANS, LES) over complex terrains. The flow solver is based on the Curvilinear Immersed Boundary (CURVIB) method to handle geometrically complex and moving domains. Different modules of the VFS package can provide different simulation capabilities for specific applications ranging from the fluid-structure interaction (FSI) of solid and deformable bodies, the two-phase free surface flow solver based on the level set method for ocean waves, sediment transport models in rivers and the large-scale models of wind farms based on actuator lines and surfaces. All numerical features of VFS package have been validated with known analytical and experimental data as reported in the related journal articles. VFS package is suitable for a broad range of engineering applications within different industries. VFS has been used in different projects with applications in wind and hydrokinetic energy, offshore and near-shore ocean studies, cardiovascular and biological flows, and natural streams and river morphodynamics. Over the last decade, the development of VFS has been supported and assisted with the help of various United States companies and federal agencies that are listed in the sponsor lists. In this version, VFS-Wind contains all the necessary modeling tools for wind energy applications, including land-based and offshore wind farms. VFS is highly scalable to run on either desktop computers or high performance clusters (up to 16,000 CPUs). This released version comes with a detailed user’s manual and a set of case studies designed to facilitate the learning of the various aspects of the code in a comprehensive manner. The included documentation and support material has been elaborated in a collaboration effort with Sandia National Labs under the contract DE-EE0005482. The VFS-Wind source code is distributed under the GNU General Public License (GPL 2.0), offering to the community the flexibility to use and expand the capabilities of the package. We note that future publications including academic journals that result from the use of VFS must be cited appropriately under the GPL v.2 license agreement.

Yang, Xiaolei↗

Structure-informed clustering for population stratification in association studies

Background: Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to the disease risk. Existing methods of population structure correction use principal component analysis or linear mixed models with a random effect when modeling associations between a trait of interest and genetic markers. However, due to stringent significance thresholds and latent interactions between the markers, these methods often fail to detect genuinely associated variants. Results: To overcome this, we propose CluStrat, which corrects for complex arbitrarily structured populations while leveraging the linkage disequilibrium induced distances between genetic markers. It performs an agglomerative hierarchical clustering using the Mahalanobis distance covariance matrix of the markers. In simulation studies, we show that our method outperforms existing methods in detecting true causal variants. Applying CluStrat on WTCCC2 and UK Biobank cohorts, we found biologically relevant associations in Schizophrenia and Myocardial Infarction. CluStrat was also able to correct for population structure in polygenic adaptation of height in Europeans. Conclusions: CluStrat highlights the advantages of biologically relevant distance metrics, such as the Mahalanobis distance, which captures the cryptic interactions within populations in the presence of LD better than the Euclidean distance.

59 BASIC BIOLOGICAL SCIENCES↗

Supporting data for climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics

This data supports the conclusions found in climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics. Included here are (i) the binarized geolocation vectors used for exhaustive vector comparisons, (ii) the resulting climatic networks, (iii) the results of applying Markov clustering to the climatic networks, and (iv) the results of applying Correlation-of-Correlations (cor-cor) to the climatic networks. The set of binarized geolocation vectors that are used as inputs for the Combinatorial Metrics library (CoMet) are of the form comet-UUUUUxVVVVV-XXXX-YYYY.shuffled.tped where UUUUU is the number of vectors, VVVVV is the length of each vector, XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a geolocation vector of binary elements A (i.e., 0) and T (i.e., 1). The set of climatic networks that are used for downstream network analysis are of the form network-U-way-XXXX-YYYY.parsed.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to an edge linking two geolocations (defined by latitude and longitude) with its corresponding edge weight (i.e., DUO score). The set of cluster results are of the form clusters-U-way-XXXX-YYYY-thresh-VVVV-inflation-WWW.clustered.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, YYYY is the ending year, VVVV is the similarity threshold, and WWW is the Markov clustering inflation rate. Each line corresponds to a single cluster and is composed of a number of corresponding geolocations (defined by latitude and longitude). The set of cor-cor results are of the form corcor-U-way-XXXX-YYYY.cumulative.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a single geolocation with it's corresponding cor-cor value.

54 ENVIRONMENTAL SCIENCES↗

Hierarchical effects facilitate spreading processes on synthetic and empirical multilayer networks

In this paper we consider the effects of corporate hierarchies on innovation spread across multilayer networks, modeled by an elaborated SIR framework. We show that the addition of management layers can significantly improve spreading processes on both random geometric graphs and empirical corporate networks. Additionally, we show that utilizing a more centralized working relationship network rather than a strict administrative network further increases overall innovation reach. In fact, this more centralized structure in conjunction with management layers is essential to both reaching a plurality of nodes and creating a stable adopted community in the long time horizon. Further, we show that the selection of seed nodes affects the final stability of the adopted community, and while the most influential nodes often produce the highest peak adoption, this is not always the case. In some circumstances, seeding nodes near but not in the highest positions in the graph produces larger peak adoption and more stable long-time adoption.

97 MATHEMATICS AND COMPUTING↗

Closeout Report ARRA supplement to DE-FG02-08ER41546, 03/15/2010 to 03/14/2011 - Advanced Transfer Map Methods for the Description of Particle Beam Dynamics

The ARRA funds were utilized to acquire a cluster of high performance computers, consisting of one Altus 2804 Server based on a Quad AMD Opteron 6174 12C with 4 2.2 GHz nodes of 12 cores each, resulting in 48 directly usable cores; as well as a Relion 1751 Server using an Intel Xeon X5677 consisting of 4 3.46 GHz cores supporting 8 threads. Both systems run the Unix flavor CentOS, which is designed for use without need of updates, which greatly enhances their reliability. The systems are used to operate our COSY INFINITY environment which supports MPI parallelization. The units arrived at MSU in September 2010, and were taken into operation shortly thereafter.

43 PARTICLE ACCELERATORS↗

A Case Study of the Glycoside Hydrolase Enzyme Mechanism Using an Automated QM-Cluster Model Building Toolkit

Glycoside hydrolase enzymes are important for hydrolyzing the β-1,4 glycosidic bond in polysaccharides for deconstruction of carbohydrates. The two-step retaining reaction mechanism of Glycoside Hydrolase Family 7 (GH7) was explored with different sized QM-cluster models built by the Residue Interaction Network ResidUe Selector (RINRUS) software using both the wild-type protein and its E217Q mutant. The first step is the glycosylation, in which the acidic residue 217 donates a proton to the glycosidic oxygen leading to bond cleavage. In the subsequent deglycosylation step, one water molecule migrates into the active site and attacks the anomeric carbon. Residue interaction-based QM-cluster models lead to reliable structural and energetic results for proposed glycoside hydrolase mechanisms. The free energies of activation for glycosylation in the largest QM-cluster models were predicted to be 19.5 and 31.4 kcal mol −1 for the wild-type protein and its E217Q mutant, which agree with experimental trends that mutation of the acidic residue Glu217 to Gln will slow down the reaction; and are higher in free energy than the deglycosylation transition states (13.8 and 25.5 kcal mol −1 for the wild-type protein and its mutant, respectively). For the mutated protein, glycosylation led to a low-energy product. This thermodynamic sink may correspond to the intermediate state which was isolated in the X-ray crystal structure. Hence, the glycosylation is validated to be the rate-limiting step in both the wild-type and mutated enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I

Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster F X , which is followed by two terminal iron–sulfur clusters F A and F B . Experiments have shown that F X has lower oxidation potential than F A and F B , which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint Em potentials of the F X , F A and F B clusters. Our calculations show that F X has the lowest oxidation potential compared to F A and F B due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for F X compared to F A and F B . Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for F X compared to both F A and F B . These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.

59 BASIC BIOLOGICAL SCIENCES↗