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At least 757 records · Page 42

The Gas-Phase Synthesis of a New Functional Hybrid Material on the Basis of Multiwalled Carbon Nanotubes Decorated with Faceted Aluminum Nanocrystals

The deposition of polyhedral aluminum nanocrystals onto the surface of multiwalled carbon nanotubes (MWCNTs) via metalorganic chemical vapor deposition with the use of triisobutylaluminum as the precursor has been performed for the first time. The new hybrid nanomaterial (Al/MWCNTs) has been characterized by X-ray phase analysis, scanning electron microscopy, and high-resolution transmission electron microscopy. The obtained Al/MWCNTs hybrid materials were tested as the filler for the creation of threedimensional composites on the basis of an AMg2 alloy via powder metallurgy. It has been shown that the use of Al/MWCNTs as the filler increases the hardness of the composites by 18% in comparison with the initial MWCNTs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Numerical Homogenization on Approach for Stokesian Suspensions

In this technical report we investigate efficient methods for numerical simulation of active suspensions. The prototypical system is a suspension of swimming bacteria in a Newtonian fluid. Rheological and other macroscopic properties of such suspensions can differ dramatically from the same properties of the suspending fluid alone or of suspensions of similar but inactive particles. Elongated bacteria, such as E. coli or B. subtilis, swim along their principal axis, propelling themselves with the help of flagella, attached at the anterior of the organism and pushing it forward in the manner of a propeller. They interact hydrodynamically with the surrounding fluid and, because of their asymmetrical shape, have the propensity to align with the local flow. This, along with the dipolar nature of bacteria (the two forces a bacterium exerts on a fluid - one due to self-propulsion and the other opposing drag - have equal magnitude and point in opposite directions), causes nearby bacteria to tend to align, resulting in a intermittent local ordering on the mesoscopic scale, which is between the microscopic scale of an individual bacterium and the macroscopic scale of the suspension (e.g., its container). The local ordering is sometimes called a collective mode or collective swimming. Thanks to self-propulsion, collective modes inject momentum into the fluid in a coherent way. This enhances the local strain rate without changing the macroscopic stress applied at the boundary of the container. The macroscopic effective viscosity of the suspension is defined roughly as the ratio of the applied stress to the bulk strain rate. If local alignment and therefore local strain-rate enhancement, are significant, the effective viscosity can be appreciably lower than that of the corresponding passive suspension or even of the surrounding fluid alone. Indeed, a sevenfold decrease in the effective viscosity was observed in experiments with B. subtilis. More generally, local collective swimming resulting from bacterial alignment can significantly alter other macroscopic properties of the suspension, such as the oxygen diffusivity and mixing rates. In order to understand the unique macroscopic properties of active suspensions the connection between microscopic swimming and alignment dynamics and the mesoscopic pattern formation must be clarified. This is difficult to do analytically in the fully general setting of moderately dense suspensions, because of the large number of bacteria involved (approx. 10 10 cm -3 in experiments) and the complex, time-dependent geometry of the system. Many reduced analytical models of bacterial have been proposed, but all of them require validation. While comparison with experiment is the ultimate test of a model's fidelity, it is difficult to conduct experiments matched to these models assumptions. Numerical simulation of the microscopic dynamics is an acceptable substitute, but it runs into the problem of having to discretize the fluid domain with a fine-grained boundary (the bacteria) and update the discretization as the domain evolves (bacteria move). This leads to a prohibitively high number of degrees of freedom and prohibitively high setup costs per timestep of simulation. In this technical report we propose numerical methods designed to alleviate these two difficulties. We indicate how to (1) construct an optimal discretization in terms of the number of degrees of freedom per digit of accuracy and (2) optimally update the discretization as the simulation evolves. The technical tool here is the derivation of rigorous error bounds on the error in the numerical solution when using our proposed discretization at the initial time as well as after a given elapsed simulation time. These error bounds should guide the construction of practical discretization schemes and update strategies. Our initial construction is carried out by using a theoretically convenient, but practically prohibitive spectral basis, which is a Galerkin basis of functions with global support. At the end of this report we propose localization techniques while maintaining acceptable error bounds. No numerical experiments were conducted as part of this study, but we envision that we may undertake such studies and further development of the method, jointly or individually.

60 APPLIED LIFE SCIENCES↗

Real-time POD-CFD Wind-Load Calculator for PV Systems

The primary objective of this project is to create an accurate web-based real-time wind-load calculator. This is of paramount importance for (1) the rapid and accurate assessments of the uplift and downforce loads on a PV mounting system, (2) identifying viable solutions from available mounting systems, and therefore helping reduce the cost of mounting hardware and installation. Wind loading calculations for structures are currently performed according to the American Society of Civil Engineers/ Structural Engineering Institute Standard ASCE/SEI 7; the values in this standard were calculated from simplified models that do not necessarily take into account relevant characteristics such as those from full 3D effects, end effects, turbulence generation and dissipation, as well as minor effects derived from shear forces on installation brackets and other accessories. This standard does not include provisions that address the special requirements of rooftop PV systems, and attempts to apply this standard may lead to significant design errors as wind loads are incorrectly estimated. Therefore, an accurate calculator would be of paramount importance for the preliminary assessments of the uplift and downforce loads on a PV mounting system, identifying viable solutions from available mounting systems, and therefore helping reduce the cost of the mounting system and installation. The challenge is that although a full-fledged three-dimensional computational fluid dynamics (CFD) analysis would properly and accurately capture the complete physical effects of air flow over PV systems, it would be impractical for this tool, which is intended to be a real-time web-based calculator. CFD routinely requires enormous computation times to arrive at solutions that can be deemed accurate and grid-independent even in powerful and massively parallel computer platforms.

14 SOLAR ENERGY↗

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), Chinook salmon ( Oncorhynchus tshawytcha ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka )] compared to the northern pike ( Esox lucius ), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λ max values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.

59 BASIC BIOLOGICAL SCIENCES↗

Cholesky-based experimental design for Gaussian process and kernel-based emulation and calibration.

Gaussian processes and other kernel-based methods are used extensively to construct approximations of multivariate data sets. The accuracy of these approximations is dependent on the data used. This paper presents a computationally efficient algorithm to greedily select training samples that minimize the weighted L p error of kernel-based approximations for a given number of data. The method successively generates nested samples, with the goal of minimizing the error in high probability regions of densities specified by users. The algorithm presented is extremely simple and can be implemented using existing pivoted Cholesky factorization methods. Training samples are generated in batches which allows training data to be evaluated (labeled) in parallel. For smooth kernels, the algorithm performs comparably with the greedy integrated variance design but has significantly lower complexity. Numerical experiments demonstrate the efficacy of the approach for bounded, unbounded, multi-modal and non-tensor product densities. We also show how to use the proposed algorithm to efficiently generate surrogates for inferring unknown model parameters from data using Bayesian inference.

97 MATHEMATICS AND COMPUTING↗

The Structure and Catalytic Mechanism of Sorghum bicolor Caffeoyl-CoA O-Methyltransferase

Caffeoyl-coenzyme A 3-O-methyltransferase (CCoAOMT) is an S-adenosyl methionine (SAM)-dependent O-methyltransferase responsible for methylation of the meta-hydroxyl group of caffeoyl-coenzyme A (CoA) on the pathway to monolignols, with their ring methoxylation status characteristic of guaiacyl or syringyl units in lignin. In order to better understand the unique class of type 2 O-methyltransferases from monocots, we have characterized CCoAOMT from sorghum (Sorghum bicolor; SbCCoAOMT), including the SAM binary complex crystal structure and steady-state enzyme kinetics. Key amino acid residues were validated with site-directed mutagenesis. Isothermal titration calorimetry data indicated a sequential binding mechanism for SbCCoAOMT, wherein SAM binds prior to caffeoyl-CoA, and the enzyme showed allosteric behavior with respect to it. 5-Hydroxyferuloyl-CoA was not a substrate for SbCCoAOMT. We propose a catalytic mechanism in which lysine-180 acts as a catalytic base and deprotonates the reactive hydroxyl group of caffeoyl-CoA. This deprotonation is facilitated by the coordination of the reactive hydroxyl group by Ca 2+ in the active site, lowering the pK a of the 3'-OH group. Collectively, these data give a new perspective on the catalytic mechanism of CCoAOMTs and provide a basis for the functional diversity exhibited by type 2 plant OMTs that contain a unique insertion loop (residues 208–231) conferring affinity for phenylpropanoid-CoA thioesters. The structural model of SbCCoAOMT can serve as the basis for protein engineering approaches to enhance the nutritional, agronomic, and industrially relevant properties of sorghum.

Walker, Alexander M.↗

Curcumin inhibits development and cell adhesion in Dictyostelium discoideum: Implications for YakA signaling and GST enzyme function

The molecular basis for nutraceutical properties of the polyphenol curcumin (Curcuma longa, Turmeric) is complex, affecting multiple factors that regulate cell signaling and homeostasis. Here, we report the effect of curcumin on cellular and developmental mechanisms in the eukaryotic model, Dictyostelium discoideum. Dictyostelium proliferation was inhibited in the presence of curcumin, which also suppressed the prestarvation marker, discoidin I, members of the yakA-mediated developmental signaling pathway, and expression of the extracellular matrix/cell adhesion proteins (DdCAD and csA). This resulted in delayed chemotaxis, adhesion, and development of the organism. In contrast to the inhibitory effects on developmental genes, curcumin induced gstA gene expression, overall GST activity, and generated production of reactive oxygen species. These studies expand our knowledge of developmental and biochemical signaling influenced by curcumin, and lends greater consideration of GST enzyme function in eukaryotic cell signaling, development, and differentiation.

60 APPLIED LIFE SCIENCES↗

Communication: Practical and rigorous reduction of the many-electron quantum mechanical Coulomb problem to O(N{sup 2/3}) storage

It is tacitly accepted that, for practical basis sets consisting of N functions, solution of the two-electron Coulomb problem in quantum mechanics requires storage of O(N{sup 4}) integrals in the small N limit. For localized functions, in the large N limit, or for planewaves, due to closure, the storage can be reduced to O(N{sup 2}) integrals. Here, it is shown that the storage can be further reduced to O(N{sup 2/3}) for separable basis functions. A practical algorithm, that uses standard one-dimensional Gaussian-quadrature sums, is demonstrated. The resulting algorithm allows for the simultaneous storage, or fast reconstruction, of any two-electron Coulomb integral required for a many-electron calculation on processors with limited memory and disk space. For example, for calculations involving a basis of 9171 planewaves, the memory required to effectively store all Coulomb integrals decreases from 2.8 Gbytes to less than 2.4 Mbytes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improving scalability of electronic structure code for molecular simulations in the presence of environment

A scalable density functional electronic code with Gaussian basis set, called UTEP-NRLMOL, is developed to perform simulations of molecular systems in the presence of the environment with particular attention to the memory requirements. In the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for density functional calculations scale as N*N, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure codes hinder their efficient usage of these platforms. We have introduced new scaling and parallelization paradigms using MPI-3 shared-memory functionality combined with usage of sparse algebra and storage of matrices in sparse format. This extends the range of applicability of the UTEP-NRLMOL code to large systems over 10,000 atoms, or using up to 67,000 basis functions, and making use of HPC architectures using over 6,000 processors utilizing all available cores. We have also interfaced code with effective fragment potential and polarizable continuum model libraries. The code was used in simulations of several applications which are published in reputed scientific journals.

74 ATOMIC AND MOLECULAR PHYSICS↗

The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔE{sub AB}. Counterpoise-corrected interaction energies ΔE{sub AB} are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A−B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [E{sub MP2/CBS}] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔE{sub CC-MP}, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔE{sub AB} with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol{sup −1}. The zero-point vibrational energy corrected estimates Δ(E{sub AB}+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D{sub 0} measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π−π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The static response function in Kohn-Sham theory: An appropriate basis for its matrix representation in case of finite AO basis sets

The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.

97 MATHEMATICS AND COMPUTING↗

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (~1.2 × 10 -3 E h / a 0 ) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comprehensive analysis of molecule-intrinsic quasi-atomic, bonding, and correlating orbitals. I. Hartree-Fock wave functions

Through a basis-set-independent web of localizing orbital-transformations, the electronic wave function of a molecule is expressed in terms of a set of orbitals that reveal the atomic structure and the bonding pattern of a molecule. The analysis is based on resolving the valence orbital space in terms of an internal space, which has minimal basis set dimensions, and an external space. In the internal space, oriented quasi-atomic orbitals and split-localized molecular orbitals are determined by new, fast localization methods. The density matrix between the oriented quasi-atomic orbitals as well as the locations of the split-localized orbitals exhibit atomic populations and inter-atomic bonding patterns. A correlation-adapted quasi-atomic basis is determined in the external orbital space. The general formulations are specified in detail for Hartree-Fock wave functions. Applications to specific molecules exemplify the general scheme.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Theoretical Benchmark of the Geometric and Optical Properties for 3d Transition Metal Nanoclusters via Density Functional Theory

Understanding structure–property relationships in atomically precise metal nanoclusters is vital in finding selective and tunable catalysts. Here, in this study, density functional theory (DFT) was used to benchmark seven exchange correlation functionals at different basis sets for 17 atomically precise nanoclusters against experimentally determined geometries, band gaps, and optical gaps. The set contains both monometallic and bimetallic clusters that possess at least two types of 3d transition metals (specifically, Cu, Ni, Fe, or Co). The benchmark highlights that PBE0 is a good functional to use regardless of the basis set, and Minnesota functionals do well with respect to specific metals. Further, while long-range corrected functionals overestimate band and optical gaps, they model absorption features better than the other considered functionals. The study additionally looks at the photoinduced hydrogen evolution reaction (HER) and the CO 2 reduction mechanism on nanoclusters reported from the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm{sup -1}) compared to experimental 0.035 eV (285.2 cm{sup -1}). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

36 MATERIALS SCIENCE↗