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At least 1,351 records · Page 75

Molecular-based analysis of nanoparticle solvation: Classical density functional approach

Proper statistical mechanics understanding of nanoparticle solvation processes requires an accurate description of the molecular structure of the solvent. Achieving this goal with standard molecular dynamics (MD) simulation methods is challenging due to large length scales. An alternative approach to this problem can be formulated using classical density functional theory (cDFT), where a full configurational description of the positions of all the atoms is replaced by collective atomic site densities in the molecule. Using an example of the negatively charged silica-like system in an aqueous polar environment represented by a two-site water model, we demonstrate here that cDFT can reproduce MD data at a fraction of the computational cost. An important implication of this result is the ability to understand how the solvent molecular features may affect the system’s properties at the macroscopic scale. A concrete example highlighted in this work is the analysis of nanoparticle interactions with sizes of up to 100 nm in diameter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Illustrated formalisms for total scattering data: a guide for new practitioners

The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.

36 MATERIALS SCIENCE↗

Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In 2 O 3 -derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Matter induced bimetric actions for gravity

Research Highlights: > Gravitational effective action in the bimetric truncation. > RG flow in the large N limit of matter coupled to gravity. > Asymptotically safe theory found in the large N expansion. - Abstract: The gravitational effective average action is studied in a bimetric truncation with a nontrivial background field dependence, and its renormalization group flow due to a scalar multiplet coupled to gravity is derived. Neglecting the metric contributions to the corresponding beta functions, the analysis of its fixed points reveals that, even on the new enlarged theory space which includes bimetric action functionals, the theory is asymptotically safe in the large N expansion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short (r O···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. Furthermore, these data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.

59 BASIC BIOLOGICAL SCIENCES↗

Fatty acid capped, metal oxo clusters as the smallest conceivable nanocrystal prototypes

Metal oxo clusters of the type M 6 O 4 (OH) 4 (OOCR) 12 (M = Zr or Hf) are valuable building blocks for materials science. Here, we synthesize a series of zirconium and hafnium oxo clusters with ligands that are typically used to stabilize oxide nanocrystals (fatty acids with long and/or branched chains). The fatty acid capped oxo clusters have a high solubility but do not crystallize, precluding traditional purification and single-crystal XRD analysis. We thus develop alternative purification strategies and we use X-ray total scattering and Pair Distribution Function (PDF) analysis as our main method to elucidate the structure of the cluster core. We identify the correct structure from a series of possible clusters (Zr3, Zr4, Zr6, Zr12, Zr10, and Zr26). Excellent refinements are only obtained when the ligands are part of the structure model. Further evidence for the cluster composition is provided by nuclear magnetic resonance (NMR), infrared spectroscopy (FTIR), thermogravimetry analysis (TGA), and mass spectrometry (MS). We find that hydrogen bonded carboxylic acid is an intrinsic part of the oxo cluster. Using our analytical tools, we elucidate the conversion from a Zr6 monomer to a Zr12 dimer (and vice versa), induced by carboxylate ligand exchange. Finally, we compare the catalytic performance of Zr12-oleate clusters with oleate capped, 5.5 nm zirconium oxide nanocrystals in the esterification of oleic acid with ethanol. The oxo clusters present a five times higher reaction rate, due to their higher surface area. Since the oxo clusters are the lower limit of downscaling oxide nanocrystals, we present them as appealing catalytic materials, and as atomically precise model systems. In addition, the lessons learned regarding PDF analysis are applicable to other areas of cluster science as well, from semiconductor and metal clusters, to polyoxometalates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of tumor-immune functional responses in a mathematical model of neoantigen cancer vaccines

Cancer neoantigen vaccines have emerged as a promising approach to stimulating the immune system to fight cancer. We propose a simple model including key elements of cancer-immune interactions and conduct a phase plane analysis to understand the immunological mechanisms of cancer neoantigen vaccines. Analytical results are obtained for two widely used functional forms that represent the killing rate of tumor cells by immune cells: the law of mass action (LMA) and the dePillis-Radunskaya Law (LPR). Using the LMA, our results reveal that a slowly growing tumor can escape the immune surveillance and that there is a unique periodic solution. The LPR offers richer dynamics, in which tumor elimination and uncontrolled tumor growth are both present. We show that tumor elimination requires sufficient number of initial activated T cells in relationship to the malignant cells, which lends support to using the neoantigen cancer vaccine as an adjuvant therapy after the primary tumor is surgically removed or treated using radiotherapy. We also derive a sufficient condition for uncontrolled tumor growth under the assumption of the LPR. Here, the juxtaposition of analyses with these two different choices for the killing rate function highlights their importance on model behavior and biological implications, by which we hope to spur further theoretical and experimental work to understand mechanisms underlying different functional forms for the killing rate.

60 APPLIED LIFE SCIENCES↗

Analysis of electron energy distribution function in the Linac4 H{sup −} source

To understand the Electron Energy Distribution Function (EEDF) in the Radio Frequency Inductively Coupled Plasmas (RF-ICPs) in hydrogen negative ion sources, the detailed analysis of the EEDFs using numerical simulation and the theoretical approach based on Boltzmann equation has been performed. It is shown that the EEDF of RF-ICPs consists of two parts, one is the low energy part which obeys Maxwellian distribution and the other is high energy part deviated from Maxwellian distribution. These simulation results have been confirmed to be reasonable by the analytical approach. The results suggest that it is possible to enhance the dissociation of molecules and the resultant H{sup −} negative ion production by reducing the gas pressure.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Building a functional, integrated GIS/remote sensing resource analysis and planning system

To be an effective tool for resource analysis and planning, a geographic information system (GIS) needs to be integrated with a digital remote sensing capability. To be truly functional, the paired system must be driven by grass roots local needs. A case study couched in a Soil Conservation District in northern Utah is presented. Agency representatives determined that the most fundamental data sets to be entered into the GIS system analysis system in the first round were: land use/land cover; geomorphic/soil unit data; hydrologic unit data; and digital terrain. The least expensive and best ways to obtain these data were determined. Data were acquired and formatted to enter the state's PRIME/ARC-INFO GIS, and are being interrogated for resource management decisions related to such issues as agricultural preservation, urban expansion, soil erosion control, and dam siting.

Ridd, M. K.↗

Oxygen Defect Configurations in Single-Phase UO 2.15

Hyperstoichiometric UO 2.15 was characterized by neutron total scattering at high temperature in the single-phase UO 2+x region of the U/O phase diagram. The diffraction data confirmed a single-phase fluorite structure at high temperature. Analysis of the short-range data showed that the same structural model does not fit the pair distribution functions well. Instead, structural models containing specific configurations of oxygen defect clusters best represent the local atomic arrangement. In conclusion, prevalent defect clusters previously proposed were fit to the experimental data, and moderately distorted oxygen cuboctahedra hypothesized by recent molecular dynamics simulations fit the data most accurately.

neutron pair-distribution function analysis↗

Size-Controlled Dissolution of Organic-Coated Silver Nanoparticles

The solubility of Ag NPs can affect their toxicity and persistence in the environment. We measured the solubility of organic-coated silver nanoparticles (Ag NPs) having particle diameters ranging from 5 to 80 nm that were synthesized using various methods, and with different organic polymer coatings including poly(vinylpyrrolidone) and gum arabic. The size and morphology of Ag NPs were characterized by transmission electron microscopy (TEM). X-ray absorption fine structure (XAFS) spectroscopy and synchrotron-based total X-ray scattering and pair distribution function (PDF) analysis were used to determine the local structure around Ag and evaluate changes in crystal lattice parameters and structure as a function of NP size. Ag NP solubility dispersed in 1 mM NaHCO{sub 3} at pH 8 was found to be well correlated with particle size based on the distribution of measured TEM sizes as predicted by the modified Kelvin equation. Solubility of Ag NPs was not affected by the synthesis method and coating as much as by their size. Based on the modified Kelvin equation, the surface tension of Ag NPs was found to be {approx}1 J/m{sup 2}, which is expected for bulk fcc (face centered cubic) silver. Analysis of XAFS, X-ray scattering, and PDFs confirm that the lattice parameter, {alpha}, of the fcc crystal structure of Ag NPs did not change with particle size for Ag NPs as small as 6 nm, indicating the absence of lattice strain. These results are consistent with the finding that Ag NP solubility can be estimated based on TEM-derived particle size using the modified Kelvin equation for particles in the size range of 5-40 nm in diameter.

36 MATERIALS SCIENCE↗

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

Here, gene fusions are the most powerful type of in silico -derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. As a result, here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli ; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. In conclusion, customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.

59 BASIC BIOLOGICAL SCIENCES↗

Hadamard products and BPS networks

We study examples of fourth-order Picard-Fuchs operators that are Hadamard products of two second-order Picard-Fuchs operators. Each second-order Picard-Fuchs operator is associated with a family of elliptic curves, and the Hadamard product computes period integrals on the fibred product of the two elliptic surfaces. We construct 3-cycles on this geometry as the union of 2-cycles in the fibre over contours on the base. We then use the special Lagrangian condition to constrain the contours on the base. This leads to a construction that is reminiscent of spectral networks and exponential networks that have previously appeared in string theory literature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Synthesis of amino-silane modified superparamagnetic Fe{sub 3}O{sub 4} nanoparticles and its application in immobilization of lipase from Pseudomonas fluorescens Lp1

Highlights: ► Magnetic nanoparticles were synthesized by chemical co-precipitation method. ► Surface was functionalized with amino-silane and used for lipase immobilization. ► Characterized through TEM, SEM, XRD, FT-IR and VSM analysis. ► The functionalization and immobilization did not affect the magnetite properties. ► The immobilized lipase showed greater functional property than free lipase. - Abstract: Superparamagnetic nanoparticles (Fe{sub 3}O{sub 4}–magnetite) were prepared by chemical co-precipitation method and their surface was functionalized with 3-aminopropyltriethoxysilane via silanization reaction to obtain amino functionalized magnetic nanoparticles. The purified lipase from Pseudomonas fluorescens Lp1 was immobilized onto functionalized magnetite using glutaraldehyde as the coupling agent. The characterization of the nanoparticles was done by scanning electron microscopy, transmission electron microscopy, powder X-ray diffraction, vibrating sample magnetometry and Fourier transformed infrared spectroscopy. The size of the magnetite was measured about 10–30 nm. The results of characterization study revealed the successful immobilization of lipase on to functionalized magnetite. The saturation magnetization of magnetic nanoparticles was found to be 28.34 emu/g whereas the immobilized magnetic nanoparticle was 17.074 emu/g. The immobilized lipase had greater activity at 50 °C and thermal stability upto 70 °C. It exhibited excellent reusability for 4 cycles and storage stability upto 15 days by retaining 75% of its initial activity.

36 MATERIALS SCIENCE↗

Independent Orbiter Assessment (IOA): Analysis of the auxiliary power unit

The results of the Independent Orbiter Assessment (IOA) of the Failure Modes and Effects Analysis (FMEA) and Critical Items List (CIL) are presented. The IOA approach features a top-down analysis of the hardware to determine failure modes, criticality, and potential critical items. To preserve independence, this analysis was accomplished without reliance upon the results contained within the NASA FMEA/CIL documentation. This report documents the independent analysis results corresponding to the Orbiter Auxiliary Power Unit (APU). The APUs are required to provide power to the Orbiter hydraulics systems during ascent and entry flight phases for aerosurface actuation, main engine gimballing, landing gear extension, and other vital functions. For analysis purposes, the APU system was broken down into ten functional subsystems. Each level of hardware was evaluated and analyzed for possible failure modes and effects. Criticality was assigned based upon the severity of the effect for each failure mode. A preponderance of 1/1 criticality items were related to failures that allowed the hydrazine fuel to escape into the Orbiter aft compartment, creating a severe fire hazard, and failures that caused loss of the gas generator injector cooling system.

Barnes, J. E.↗

Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon

The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.

Plant Sciences↗