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At least 811 records · Page 45

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of reversible dislocation-based deformation on nanoparticle strain at failure

Molecular dynamics simulations are used to isolate and quantify the reversible and irreversible mechanisms that contribute to deformation in platinum nanoparticles under compression. Quantitative analysis reveals how the nucleation and entanglement of dislocations can lead to reversible dislocation-based deformation. Simulations run at different temperatures and loading conditions show that the formation of entangled dislocations is more likely at higher temperatures and is facilitated by loading orientations where dislocations nucleate on intersecting slip planes. The presence of entangled dislocations increases the strain at failure due to the ability of those dislocations to accommodate strain reversibly. The results are corroborated by the observation of similar entangled dislocation loops during in situ compression experiments on nanoparticles of the same material. Altogether, these findings provide insight into the role of dislocations in both reversible and irreversible deformation and their implications for nanoparticle stability and properties.

36 MATERIALS SCIENCE↗

Structure and mechanical properties of grain boundaries in molybdenum disulfide (MoS 2 )

Molybdenum disulfide (MoS 2 ) is a two-dimensional material widely used as a lubricant in many applications involving mechanical loading under a wide range of operating temperatures. Since many synthesis and processing techniques yield MoS 2 in its polycrystalline form, establishing grain boundary (GB) structure–property relations is key to designing MoS 2 microstructures with tailored properties. Here, we employ classical, reactive atomistic simulations to investigate the structure and mechanical behavior of a wide range of GBs in MoS 2 as a function of temperature. Using a bicrystal MoS 2 geometry, we characterize the atomic structure and calculate the energy of several low-angle GBs. Then, we simulate the tensile deformation behavior of MoS 2 bicrystals at several temperatures. Our results reveal that at temperatures above 100 K, the deformation of MoS 2 bicrystals is characterized by the nucleation of shear bands from GBs that grow, with subsequent loading, into the MoS 2 crystals. At low temperatures, the tensile deformation is characterized by the nucleation and propagation of deformation fronts, resulting in altered bond angles and bond lengths. Quantitative analysis reveals a decrease in the ultimate tensile stress and ultimate failure strain of MoS 2 bicrystals with the increase in temperature. Furthermore, our simulations of the mechanical behavior of metastable GBs reveal that the strength and ductility decrease with the increase in energy of these boundary structures. In broad terms, our work provides future avenues to employ GB engineering as a strategy to tailor the properties of MoS 2 microstructures.

Moore, Robert D. [Lehigh Univ., Bethlehem, PA (Uni↗

Ultraviolet H 2 luminescence in molecular clouds induced by cosmic rays

Context. Galactic cosmic rays (CRs) play a crucial role in ionisation, dissociation, and excitation processes within dense cloud regions where UV radiation is absorbed by dust grains and gas species. CRs regulate the abundance of ions and radicals, leading to the formation of more and more complex molecular species, and determine the charge distribution on dust grains. A quantitative analysis of these effects is essential for understanding the dynamical and chemical evolution of star-forming regions. Aims. The CR-induced photon flux has a significant impact on the evolution of the dense molecular medium in its gas and dust components. This study evaluates the flux of UV photons generated by CRs to calculate the photon-induced dissociation and ionisation rates of a vast number of atomic and molecular species, as well as the integrated UV photon flux. Methods. To achieve these goals, we took advantage of recent developments in the determination of the spectra of secondary electrons, in the calculation of state-resolved excitation cross sections of H 2 by electron impact, and of photodissociation and photoionisation cross sections. Results. We calculated the H 2 level population of each rovibrational level of the X, B, C, B′, D, B″, D′, and a states. We then computed the UV photon spectrum of H 2 in its line and continuum components between 72 and 700 nm, with unprecedented accuracy, as a function of the CR spectrum incident on a molecular cloud, the H 2 column density, the isomeric H 2 composition, and the dust properties. The resulting photodissociation and photoionisation rates are, on average, lower than previous determinations by a factor of about 2, with deviations of up to a factor of 5 for the photodissociation of species such as AlH, C 2 H 2 , C 2 H 3 , C 3 H 3 , LiH, N 2 , NaCl, NaH, O 2 + , S2, SiH, l-C 4 , and l-C 5 H. A special focus is given to the photoionisation rates of H 2 , HF, and N 2 , as well as to the photodissociation of H 2 , which we find to be orders of magnitude higher than previous estimates. We give parameterisations for both the photorates and the integrated UV photon flux as a function of the CR ionisation rate, which implicitly depends on the H 2 column density, as well as the dust properties.

79 ASTRONOMY AND ASTROPHYSICS↗

Recent progress with the top to bottom approach to vectorization in GeantV

SIMD acceleration can potentially boost by factors the application throughput. Achieving efficient SIMD vectorization for scalar code with complex data flow and branching logic, goes however way beyond breaking some loop dependencies and relying on the compiler. Since the refactoring effort scales with the number of lines of code, it is important to understand what kind of performance gains can be expected in such complex cases. We started to investigate a couple of years ago a top to bottom vectorization approach to particle transport simulation. Percolating vector data to algorithms was mandatory since not all the components can internally vectorize. Vectorizing low-level algorithms is certainly necessary, but not sufficient to achieve relevant SIMD gains. In addition, the overheads for maintaining the concurrent vector data flow and copy data have to be minimized. In the context of a vectorization R&D for simulation we developed a framework to allow different categories of scalar and vectorized components to co-exist, dealing with data flow management and real-time heuristic optimizations. The paper describes our approach on coordinating SIMD vectorization at framework level, making a detailed quantitative analysis of the SIMD gain versus overheads, with a breakdown by components in terms of geometry, physics and magnetic field propagation. We also present the more general context of this R&D work and goals for 2018.

97 MATHEMATICS AND COMPUTING↗

Interpreting plasmonic response of epitaxial Ag/Si(100) island ensembles

Associating features in the experimentally measured optical response of epitaxial Ag islands grown on Si(100) with the localized surface plasmon resonances (LSPRs) hosted by the Ag islands is challenging due to the variation of the Si dielectric function over the energy range under consideration. However, it is possible to conclusively identify features in the experimental spectra with LSPR modes oscillating both parallel and perpendicular to the epitaxial interface by simulating the optical response. The Abeles matrix method is used to describe the composite layered system and the Ag islands are modeled using the thin island film model developed by Bedeaux and Vlieger. By incorporating island morphology parameters determined by quantitative analysis of electron micrographs, the simulation faithfully reproduces the main features of the experimental spectra. Individually zeroing the dipoles associated with the LSPR modes enables conclusive identification of their contribution to the optical response of the composite system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Infrared spectroscopic investigation of nuclear spin conversion in solid CH{sub 4}

Infrared spectra of solid CH{sub 4} were studied in the ν{sub 3} and ν{sub 4} vibrational regions. The phase I crystal around 30 K showed broad absorption bands, whereas the phase II crystal at 6.9–10.3 K exhibited splitting of these bands after annealing above 20 K. The split peaks were assigned to the librating and almost freely rotating molecules in phase II on the basis of the peak spacings and time evolution of the peak intensities. From the quantitative analysis of the temporal changes of the R(0) and R(1) peak intensities, the relaxation rates of the numbers of molecules with J = 0 (I = 2) and J = 1 (I = 1) were determined in the temperature range of 6.9–10.3 K. We fitted the function resulting from a combination of direct and indirect relaxation processes mediated by phonons to the temperature dependence of these rates and obtained the activation energies of the indirect process: C ≃ 36 K. Since this value is higher than the energies of perturbed J = 2 states relative to the J = 1 state, we argue that the nuclear spin conversion through the J = 3 state also takes place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterizing nanoscale scanning probes using electron microscopy: A novel fixture and a practical guide

The nanoscale geometry of probe tips used for atomic force microscopy (AFM) measurements determines the lateral resolution, contributes to the strength of the tip-surface interaction, and can be a significant source of uncertainty in the quantitative analysis of results. While inverse imaging of the probe tip has been used successfully to determine probe tip geometry, direct observation of the tip profile using electron microscopy (EM) confers several advantages: it provides direct (rather than indirect) imaging, requires fewer algorithmic parameters, and does not require bringing the tip into contact with a sample. In the past, EM-based observation of the probe tip has been achieved using ad hoc mounting methods that are constrained by low throughput, the risk of contamination, and repeatability issues. We report on a probe fixture designed for use in a commercial transmission electron microscope that enables repeatable mounting of multiple AFM probes as well as a reference grid for beam alignment. This communication describes the design, fabrication, and advantages of this probe fixture, including full technical drawings for machining. Further, best practices are discussed for repeatable, non-destructive probe imaging. Finally, examples of the fixture’s use are described, including characterization of common commercial AFM probes in their out-of-the-box condition.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Charge transfer in dissociating iodomethane and fluoromethane molecules ionized by intense femtosecond X-ray pulses

Ultrafast electron transfer in dissociating iodomethane and fluoromethane molecules was studied at the Linac Coherent Light Source free-electron laser using an ultraviolet pump, X-ray-probe scheme. The results for both molecules are discussed with respect to the nature of their UV excitation and different chemical properties. Signatures of long distance intramolecular charge transfer are observed for both species, and a quantitative analysis of its distance dependence in iodomethane is carried out for charge states up to I 21þ. The reconstructed critical distances for electron transfer are in good agreement with a classical over-the-barrier model and with an earlier experiment employing a near infrared pump pulse. VC 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http:// creativecommons.org/licenses/by/4.0/). [http://dx.doi.org/10.1063/1.4944344]

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bifurcation, chaos, and scan instability in dynamic atomic force microscopy

The dynamical motion at any point on the cantilever of an atomic force microscope can be expressed quite generally as a superposition of simple harmonic oscillators corresponding to the vibrational modes allowed by the cantilever shape. Central to the dynamical equations is the representation of the cantilever-sample interaction force as a polynomial expansion with coefficients that account for the interaction force “stiffness,” the cantilever-to-sample energy transfer, and the displacement amplitude of cantilever oscillation. Renormalization of the cantilever beam model shows that for a given cantilever drive frequency cantilever dynamics can be accurately represented by a single nonlinear mass-spring model with frequency-dependent stiffness and damping coefficients [S. A. Cantrell and J. H. Cantrell, J. Appl. Phys. 110, 094314 (2011)]. Application of the Melnikov method to the renormalized dynamical equation is shown to predict a cascade of period doubling bifurcations with increasing cantilever drive force that terminates in chaos. The threshold value of the drive force necessary to initiate bifurcation is shown to depend strongly on the cantilever setpoint and drive frequency, effective damping coefficient, nonlinearity of the cantilever-sample interaction force, and the displacement amplitude of cantilever oscillation. The model predicts the experimentally observed interruptions of the bifurcation cascade for cantilevers of sufficiently large stiffness. Operational factors leading to the loss of image quality in dynamic atomic force microscopy are addressed, and guidelines for optimizing scan stability are proposed using a quantitative analysis based on system dynamical parameters and choice of feedback loop parameter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Diffusive flux in a model of stochastically gated oxygen transport in insect respiration

Oxygen delivery to insect tissues is controlled by transport through a branched tubular network that is connected to the atmosphere by valve-like gates, known as spiracles. In certain physiological regimes, the spiracles appear to be randomly switching between open and closed states. Quantitative analysis of this regime leads a reaction-diffusion problem with stochastically switching boundary condition. We derive an expression for the diffusive flux at long times in this problem. Our approach starts with the derivation of the passage probability for a single particle that diffuses between a stochastically gated boundary, which models the opening and closing spiracle, and the perfectly absorbing boundary, which models oxygen absorption by the tissue. This passage probability is then used to derive an expression giving the diffusive flux as a function of the geometric parameters of the tube and characteristic time scales of diffusion and gate dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Kelvin-Helmholtz instability of boundary-layer plasmas in the kinetic regime

The dynamics of the Kelvin-Helmholtz instability are investigated in the kinetic, high-frequency regime with a novel, two-dimensional, mesh-free tree code. In contrast to earlier studies which focused on specially prepared equilibrium configurations in order to compare with fluid theory, a more naturally occurring plasma-vacuum boundary layer is considered here with relevance to both space plasma and linear plasma devices. Quantitative comparisons of the linear phase are made between the fluid and kinetic models. After establishing the validity of this technique via comparison to linear theory and conventional particle-in-cell simulation for classical benchmark problems, a quantitative analysis of the more complex magnetized plasma-vacuum layer is presented and discussed. It is found that in this scenario, the finite Larmor orbits of the ions result in significant departures from the effective shear velocity and width underlying the instability growth, leading to generally slower development and stronger nonlinear coupling between fast growing short-wavelength modes and longer wavelengths.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dependency of the Reynolds number on the water flow through the perforated tube

Safe and effective loading of nuclear reactor fuel assemblies demands qualitative and quantitative analysis of the relationship between the coolant temperature in the fuel assembly outlet, measured by the thermocouple, and the mean coolant temperature profile in the thermocouple plane position. It is not possible to perform the analysis directly in the reactor, so it is carried out using measurements on the physical model, and the CFD fuel assembly coolant flow models. The CFD models have to be verified and validated in line with the temperature and velocity profile obtained from the measurements of the cooling water flowing in the physical model of the fuel assembly. Simplified physical model with perforated central tube and its validated CFD model serve to design of the second physical model of the fuel assembly of the nuclear reactor VVER 440. Physical model will be manufactured and installed in the laboratory of the Institute of Energy Machines, Faculty of Mechanical Engineering of the Slovak University of Technology in Bratislava.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Synthesis of FeCoNi nanoparticles by galvanostatic technique

Soft magnetic nanoparticles of FeCoNi have been becoming interesting objects for many researchers due to its potential application in electronic devices. One of the most promising methods for material preparation is the electrodeposition which capable of growing nanoparticles alloy directly onto the substrate. In this paper, we report our electrodeposition studies on nanoparticles synthesis using galvanostatic electrodeposition technique. Chemical composition of the synthesized FeCoNi was successfully controlled through the adjustment of the applied currents. It is revealed that the content of each element, obtained from quantitative analysis using atomic absorption spectrometer (AAS), could be modified by the adjustment of current in which Fe and Co content decreased at larger applied currents, while Ni content increased. The nanoparticles of Co-rich FeCoNi and Ni-rich FeCoNi were obtained from sulphate electrolyte at the range of applied current investigated in this work. Broad diffracted peaks in the X-ray diffractograms indicated typical nanostructures of the solid solution of FeCoNi.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Experimental evaluation of the response of micro-channel plate detector to ions with 10s of MeV energies

The absolute calibration of a microchannel plate (MCP) assembly using a Thomson spectrometer for laser-driven ion beams is described. In order to obtain the response of the whole detection system to the particles’ impact, a slotted solid state nuclear track detector (CR-39) was installed in front of the MCP to record the ions simultaneously on both detectors. The response of the MCP (counts/particles) was measured for 5–58 MeV carbon ions and for protons in the energy range 2–17.3 MeV. The response of the MCP detector is non-trivial when the stopping range of particles becomes larger than the thickness of the detector. Protons with energies E ≳ 10 MeV are energetic enough that they can pass through the MCP detector. Quantitative analysis of the pits formed in CR-39 and the signal generated in the MCP allowed to determine the MCP response to particles in this energy range. Moreover, a theoretical model allows to predict the response of MCP at even higher proton energies. This suggests that in this regime the MCP response is a slowly decreasing function of energy, consistently with the decrease of the deposited energy. These calibration data will enable particle spectra to be obtained in absolute terms over a broad energy range.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Enhanced information content for three-dimensional localization and tracking using the double-helix point spread function with variable-angle illumination epifluorescence microscopy

The signal-to-noise ratio (SNR) and three-dimensional localization precision of a double helix point spread function (DH-PSF) can be significantly improved by applying variable-angle illumination epifluorescence microscopy (VAI, also commonly known as “pseudo-TIRF” or “quasi-TIRF”). In this paper, we performed a quantitative analysis of the dependence of SNR and localization precision on the number of measured photons and the incident angle for static particles under both low (at a planar index-matched interface) and high (within a porous silica matrix) fluorescent background conditions. We found that under noisier imaging conditions, the SNR and localization precision obtained using VAI are up to fivefold and threefold greater, respectively, than those obtained using epi-illumination. Finally and moreover, we demonstrate that the combination of DH-PSF and VAI can significantly improve the accuracy of the measured diffusion coefficient for mobile particles, even at a relatively large distance (50 μm) from the boundary of the optical cell.

42 ENGINEERING↗

Thermal diffusivity determination using heterodyne phase insensitive transient grating spectroscopy

The elastic and thermal transport properties of opaque materials may be measured using transient grating spectroscopy (TGS) by inducing and monitoring periodic excitations in both reflectivity and surface displacement. The “phase grating” response encodes both properties of interest, but complicates quantitative analysis by convolving temperature dynamics with surface displacement dynamics. Hence, thermal transport characteristics are normally determined using the “amplitude grating” response to isolate the surface temperature dynamics. Yet, this signal character requires absolute heterodyne phase calibration and contains no elastic property information. Here, a method is developed by which phase grating TGS measurements may be consistently analyzed to determine thermal diffusivity with no prior knowledge of the expected properties. To demonstrate this ability, the wavelength-dependent 1D effective thermal diffusivity of pure germanium is measured using this type of response and found to be consistent with theoretical predictions made by solving the Boltzmann transport equation. This ability to determine the elastic and thermal properties from a single set of TGS measurements will be particularly advantageous for new in situ implementations of the technique being used to study dynamic materials systems.

36 MATERIALS SCIENCE↗

Swelling of individual nanodomains in hydrated block copolymer electrolyte membranes

Here, we examine the swelling of nanostructured block copolymer electrolytes immersed in liquid water. A series of sulfonated polystyrene-b-polyethylene-b-polystyrene (S-SES) membranes having the same nominal chemical composition but two different morphologies are prepared by systematic changes in processing. We start with a membrane comprising a mixture of homopolymer polystyrene (hPS) and a polystyrene-b-polyethylene-b-polystyrene (SES) copolymer. hPS is subsequently selectively removed from the membrane and the polystyrene domains are sulfonated to give S-SES membranes. The morphology of the membranes is controlled by controlling Φ v , the volume fraction of hPS in the blended membrane. The morphology of the membranes was studied by small angle X-ray scattering (SAXS), cryogenic scanning transmission electron microscopy (cryo-STEM), and cryogenic electron tomography. The overall domain swelling measured by SAXS decreases slightly at Φ v = 0.29; a crossover from lamellar to bicontinuous morphology is obtained at the same value of Φ v . The bicontinuous morphologies absorb more water than the lamellar morphologies. By contrast, the nanodomain swelling of the bicontinuous membrane (120%) is slightly less than that of the lamellar membrane (150%). Quantitative analysis of the STEM images and electron tomography was used to determine the swelling on the hydrophilic and hydrophobic domains due to exposure to water. The hydrophilic sulfonated polystyrene-rich domain spacing increases while the hydrophobic polyethylene domain spacing decreases when the membranes are hydrated. The extent of increase and decrease is not a strong function of Φ v .

36 MATERIALS SCIENCE↗