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At least 1,135 records · Page 63

An analysis of hydrated proton diffusion in ab initio molecular dynamics

A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore, the correlations of the neighboring water atoms are identified as the fourth water approaches the hydronium. Finally, the temperature effects on structural and dynamical properties are studied.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Laser Spectroscopic and Theoretical Studies of the Structures and Encapsulation Motifs of Functional Molecules

Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes

electronic structure calculations↗

Enhanced third harmonic generation from the epsilon-near-zero modes of ultrathin films

We experimentally demonstrate efficient third harmonic generation from an indium tin oxide nanofilm (λ/42 thick) on a glass substrate for a pump wavelength of 1.4 μm. A conversion efficiency of 3.3 × 10{sup −6} is achieved by exploiting the field enhancement properties of the epsilon-near-zero mode with an enhancement factor of 200. This nanoscale frequency conversion method is applicable to other plasmonic materials and reststrahlen materials in proximity of the longitudinal optical phonon frequencies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Three-dimensional simulation of H-mode plasmas with localized divertor impurity injection on Alcator C-Mod using the edge transport code EMC3-EIRENE

Experiments in Alcator C-Mod to assess the level of toroidal asymmetry in divertor conditions resulting from poloidally and toroidally localized extrinsic impurity gas seeding show a weak toroidal peaking (∼1.1) in divertor electron temperatures for high-power enhanced D-alpha H-mode plasmas. This is in contrast to similar experiments in Ohmically heated L-mode plasmas, which showed a clear toroidal modulation in the divertor electron temperature. Modeling of these experiments using the 3D edge transport code EMC3-EIRENE [Y. Feng et al., J. Nucl. Mater. 241, 930 (1997)] qualitatively reproduces these trends, and indicates that the different response in the simulations is due to the ionization location of the injected nitrogen. Low electron temperatures in the private flux region (PFR) in L-mode result in a PFR plasma that is nearly transparent to neutral nitrogen, while in H-mode the impurities are ionized in close proximity to the injection location, with this latter case yielding a largely axisymmetric radiation pattern in the scrape-off-layer. The consequences for the ITER gas injection system are discussed. Quantitative agreement with the experiment is lacking in some areas, suggesting potential areas for improving the physics model in EMC3-EIRENE.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Using an energized oxygen micro-jet for improved graphene etching by focused electron beam

We report on an improved Focused Electron Beam Induced Etching (FEBIE) process, which exploits heated oxygen delivery via a continuous supersonic micro-jet resulting in faster graphene patterning and better etch feature definition. Positioning a micro-jet in close proximity to a graphene surface with minimal jet spreading due to a continuous regime of gas flow at the exit of the 10 μm inner diameter capillary allows for focused exposure of the surface to reactive oxygen at high mass flux and impingement energy of a supersonic gas stream localized to a small etching area exposed to electron beam. These unique benefits of focused supersonic oxygen delivery to the surface enable a dramatic increase in the etch rate of graphene with no parasitic carbon “halo” deposition due to secondary electrons from backscattered electrons (BSE) in the area surrounding the etched regions. Increase of jet temperature via local nozzle heating provides means for enhancing kinetic energy of impinging oxygen molecules, which further speed up the etch, thus minimizing the beam exposure time and required electron dose, before parasitic carbon film deposition due to BSE mediated decomposition of adsorbed hydrocarbon contaminants has a measurable impact on quality of graphene etched features. Interplay of different physical mechanisms underlying an oxygen micro-jet assisted FEBIE process is discussed with support from experimental observations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Surface hopping investigation of the relaxation dynamics in radical cations

Ionization processes can lead to the formation of radical cations with population in several ionic states. In this study, we examine the dynamics of three radical cations starting from an excited ionic state using trajectory surface hopping dynamics in combination with multiconfigurational electronic structure methods. The efficiency of relaxation to the ground state is examined in an effort to understand better whether fragmentation of cations is likely to occur directly on excited states or after relaxation to the ground state. The results on cyclohexadiene, hexatriene, and uracil indicate that relaxation to the ground ionic state is very fast in these systems, while fragmentation before relaxation is rare. Ultrafast relaxation is facilitated by the close proximity of electronic states and the presence of two- and three-state conical intersections. Examining the properties of the systems in the Franck-Condon region can give some insight into the subsequent dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t{sub 1} and t{sub 3} periods, respectively. In addition to through-space and through-bond {sup 13}C/{sup 1}H and {sup 13}C/{sup 13}C chemical shift correlations, the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment also provides a COSY-type {sup 1}H/{sup 1}H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ({sup 1}H/{sup 1}H chemical shift correlation spectrum) at different {sup 13}C chemical shift frequencies from the 3D {sup 1}H/{sup 13}C/{sup 1}H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymerization of defect states at dislocation cores in InAs

Dislocations are essentially lines of point defects which can act as recombination centers in semiconductor devices. These point defects do not behave as isolated defects. Their spatial proximity enables them to hybridize into a one-dimensional band, and the distribution of resulting defect-band states is determined by both the position of the band and its dispersion. In the case of glissile 90° partial dislocations in III-V semiconductors, the dislocation core can adopt a variety of different reconstructions. Each of these reconstructions has a different arrangement of point defects, which affects the hybridization into defect bands and their associated dispersion. Here, we illustrate these principles by performing first-principles calculations for InAs and find that some defect levels for InAs dislocations lie outside of the band gap where they cannot act as recombination centers. To provide some insight into the electronic structure of dislocations in ternary alloys, some examples relevant to InGaAs and GaAsP are included.

36 MATERIALS SCIENCE↗

Note: Spin-exchange optical pumping in a van

The advent of spin-hyperpolarization techniques designed to overcome the sensitivity issue of nuclear magnetic resonance owing to polarization transfer from more ordered systems has recently raised great enthusiasm. However, the out-of-equilibrium character of the polarization requires a close proximity between the area of production and the site of use. We present here a mobile spin-exchange optical pumping setup that enables production of laser-polarized noble gases in a standalone mode, in close proximity to hospitals or research laboratories. Only compressed air and mains power need to be supplied by the host laboratory.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Soft x-ray ptychography studies of nanoscale magnetic and structural correlations in thin SmCo 5 films

High spatial resolution magnetic x-ray spectromicroscopy at x-ray photon energies near the cobalt L 3 resonance was applied to probe an amorphous 50 nm thin SmCo 5 film prepared by off-axis pulsed laser deposition onto an x-ray transparent 200 nm thin Si 3 N 4 membrane. Alternating gradient magnetometry shows a strong in-plane anisotropy and an only weak perpendicular magnetic anisotropy, which is confirmed by magnetic transmission soft x-ray microscopy images showing over a field of view of 10 μm a primarily stripe-like domain pattern but with local labyrinth-like domains. Soft x-ray ptychography in amplitude and phase contrast was used to identify and characterize local magnetic and structural features over a field of view of 1 μm with a spatial resolution of about 10 nm. There, the magnetic labyrinth domain patterns are accompanied by nanoscale structural inclusions that are primarily located in close proximity to the magnetic domain walls. In conclusion, our analysis suggests that these inclusions are nanocrystalline Sm 2 Co 17 phases with nominally in-plane magnetic anisotropy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-shell model of ion-induced nucleic acid condensation

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.”.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The thermodynamic and kinetic interactions of He interstitial clusters with bubbles in W

Due to its enviable properties, tungsten is a leading candidate plasma facing material in nuclear fusion reactors. However, like many other metals, tungsten is known to be affected by the high doses of helium atoms incoming from the plasma. Indeed, the implanted interstitial helium atoms cluster together and, upon reaching a critical cluster size, convert into substitutional nanoscale He bubbles. These bubbles then grow by absorbing further interstitial clusters from the matrix. This process can lead to deleterious changes in microstructure, degradation of mechanical properties, and contamination of the plasma. In order to better understand the growth process, we use traditional and accelerated molecular dynamics simulations to investigate the interactions between interstitial He clusters and pre-existing bubbles. These interactions are characterized in terms of thermodynamics and kinetics. We show that the proximity of the bubble leads to an enhancement of the trap mutation rate and, consequently, to the nucleation of satellite bubbles in the neighborhood of existing ones. We also uncover a number of mechanisms that can lead to the subsequent annihilation of such satellite nanobubbles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Time-dependent analysis of visible helium line-ratios for electron temperature and density diagnostic using synthetic simulations on NSTX-U

Helium line-ratios for electron temperature (T{sub e}) and density (n{sub e}) plasma diagnostic in the Scrape-Off-Layer (SOL) and edge regions of tokamaks are widely used. Due to their intensities and proximity of wavelengths, the singlet, 667.8 and 728.1 nm, and triplet, 706.5 nm, visible lines have been typically preferred. Time-dependency of the triplet line (706.5 nm) has been previously analyzed in detail by including transient effects on line-ratios during gas-puff diagnostic applications. In this work, several line-ratio combinations within each of the two spin systems are analyzed with the purpose of eliminating transient effects to extend the application of this powerful diagnostic to high temporal resolution characterization of plasmas. The analysis is done using synthetic emission modeling and diagnostic for low electron density NSTX SOL plasma conditions by several visible lines. Quasi-static equilibrium and time-dependent models are employed to evaluate transient effects of the atomic population levels that may affect the derived electron temperatures and densities as the helium gas-puff penetrates the plasma. The analysis of a wider range of spectral lines will help to extend this powerful diagnostic to experiments where the wavelength range of the measured spectra may be constrained either by limitations of the spectrometer or by other conflicting lines from different ions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Domain wall and interphase boundary motion in (1−x)Bi(Mg{sub 0.5}Ti{sub 0.5})O{sub 3}–xPbTiO{sub 3} near the morphotropic phase boundary

Electric field-induced changes in the domain wall motion of (1−x)Bi(Mg{sub 0.5}Ti{sub 0.5})O{sub 3}–xPbTiO{sub 3} (BMT-xPT) near the morphotropic phase boundary (MPB) where x = 0.37 (BMT-37PT) and x = 0.38 (BMT-38PT), are studied by means of synchrotron x-ray diffraction. Through Rietveld analysis and profile fitting, a mixture of coexisting monoclinic (Cm) and tetragonal (P4mm) phases is identified at room temperature. Extrinsic contributions to the property coefficients are evident from electric-field-induced domain wall motion in both the tetragonal and monoclinic phases, as well as through the interphase boundary motion between the two phases. Domain wall motion in the tetragonal and monoclinic phases for BMT-37PT is larger than that of BMT-38PT, possibly due to this composition's closer proximity to the MPB. Increased interphase boundary motion was also observed in BMT-37PT. Lattice strain, which is a function of both intrinsic piezoelectric strain and elastic interactions of the grains (the latter originating from domain wall and interphase boundary motion), is similar for the respective tetragonal and monoclinic phases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of the metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ∼1.3 m s{sup −1} to ∼2.5 m s{sup −1} during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s{sup −1} have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. Using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

X-ray magnetic circular dichroism and near-edge X-ray absorption fine structure of buried interfacial magnetism measured by using a scanning tunneling microscope tip

Magnetism at buried interfaces plays a crucial role in many emerging phenomena, but detection of interfacial magnetism in close proximity to a surface with elemental and chemical sensitivity is a challenging task. Here, we use a low temperature synchrotron x-ray scanning tunneling microscopy to investigate x-ray magnetic circular dichroism and near edge x-ray absorption fine structure of La 0.67 Sr 0.33 MnO 3 -LaNiO 3 superlattices in the absence of a magnetic field. In stark contrast to the weak magnetic signal of Mn when the La 0.67 Sr 0.33 MnO 3 layers are located on top, a robust x-ray magnetic circular dichroism signal is detected when they are buried underneath the LaNiO 3 layers. The near edge x-ray absorption fine structure reveals the valence states of the manganese while the oxygen K- edge x-ray absorption spectra show an increase in hole formation indicating a cogent charge transfer at the LaNiO 3 /La 0.67 Sr 0.33 MnO 3 interface. This work demonstrates that scanning tunneling microscopy can be extended to the synchrotron X-ray study of buried interfaces by controlling the sample-tip (e.g., detector) separation in the nanometer regime. The close sample-tip proximity further provides a path toward probing of small lateral areas with zero-field measurements in multi-domain samples.

36 MATERIALS SCIENCE↗

Ion-temperature determination with a baffled Langmuir probe

An electrostatic Langmuir probe for real-time measurements of parameters in magnetized plasma is tested in fully ionized, barium, Q-machine plasma. The small-diameter, long-length, tungsten wire sensor, i.e., the probe tip, oriented with its cylindrical axis perpendicular to the magnetic field (B), is partially shielded by ceramic baffles, or masks, that form sensor-access slots between the baffles. Adjusting the azimuthal orientation of the slots, by rotating the probe about its cylindrical axis, changes the fraction of proximity gyro-orbiting electrons, relative to the fraction of proximity gyro-orbiting ions, that can access the recessed sensor along the magnetic field. Thus, the ratio between the electron and ion saturation currents, $I^{sat}_e$ and $I^{sat}_i$, can be adjusted without having affected the probe bias voltage V b . When optimally shielded ($I^{sat}_e/I^{sat}_i$=1), accurate, real-time measurements of space potential Vs can be acquired. When maximally shielded ($I^{sat}_e/I^{sat}_i$ << 1), accurate, real-time measurements of ion temperature T i can be acquired. Subtracting the floating potential V f of an optimally shielded baffled probe from V f of a maximally shielded baffled probe yields T i (and its fluctuation phase) in real time.

47 OTHER INSTRUMENTATION↗

Visualizing Key Hinges and a Potential Major Source of Compliance in the Lever Arm of Myosin

We have determined the 2.3-{angstrom}-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch ('smooth') muscle. This structure reveals hinges that may function in the 'on' and 'off' states of myosin. The molecule adopts two different conformations about the heavy chain 'hook' and regulatory light chain (RLC) helix D. This conformational change results in extended and compressed forms of the lever arm whose lengths differ by 10 {angstrom}. The heavy chain hook and RLC helix D hinges could thus serve as a potential major and localized source of cross-bridge compliance during the contractile cycle. In addition, in one of the molecules of the crystal, part of the RLC N-terminal extension is seen in atomic detail and forms a one-turn alpha-helix that interacts with RLC helix D. This extension, whose sequence is highly variable in different myosins, may thus modulate the flexibility of the lever arm. Moreover, the relative proximity of the phosphorylation site to the helix D hinge suggests a potential role for conformational changes about this hinge in the transition between the on and off states of regulated myosins.

59 BASIC BIOLOGICAL SCIENCES↗