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At least 1,081 records · Page 60

Accuracy of buffered-force QM/MM simulations of silica

We report comparisons between energy-based quantum mechanics/molecular mechanics (QM/MM) and buffered force-based QM/MM simulations in silica. Local quantities—such as density of states, charges, forces, and geometries—calculated with both QM/MM approaches are compared to the results of full QM simulations. We find the length scale over which forces computed using a finite QM region converge to reference values obtained in full quantum-mechanical calculations is ∼10 Å rather than the ∼5 Å previously reported for covalent materials such as silicon. Electrostatic embedding of the QM region in the surrounding classical point charges gives only a minor contribution to the force convergence. While the energy-based approach provides accurate results in geometry optimizations of point defects, we find that the removal of large force errors at the QM/MM boundary provided by the buffered force-based scheme is necessary for accurate constrained geometry optimizations where Si–O bonds are elongated and for finite-temperature molecular dynamics simulations of crack propagation. Moreover, the buffered approach allows for more flexibility, since special-purpose QM/MM coupling terms that link QM and MM atoms are not required and the region that is treated at the QM level can be adaptively redefined during the course of a dynamical simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories in a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

X-ray beam compression by tapered waveguides

We have fabricated linear tapered waveguide channels filled with air and imbedded in silicon for the hard x-ray regime, using a processing scheme involving e-beam lithography, reactive ion etching, and wafer bonding. Beam compression in such channels is demonstrated by coupling a pre-focused undulator beam into the channels, and recording the exit flux and far-field diffraction patterns. We achieved a compressed beam with a spot size of 16.48 nm (horizontal) × 14.6 nm (vertical) near the waveguide exit plane, as determined from the reconstructed near-field distribution, at an exit flux which is eight times higher than that of an equivalent straight channel. Simulations indicate that this gain could reach three to four orders of magnitude for longer channels with tapering in two directions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stable oscillation in spin torque oscillator excited by a small in-plane magnetic field

Theoretical conditions to excite self-oscillation in a spin torque oscillator consisting of a perpendicularly magnetized free layer and an in-plane magnetized pinned layer are investigated by analytically solving the Landau-Lifshitz-Gilbert equation. The analytical relation between the current and oscillation frequency is derived. It is found that a large amplitude oscillation can be excited by applying a small field pointing to the direction anti-parallel to the magnetization of the pinned layer. The validity of the analytical results is confirmed by comparing with numerical simulation, showing good agreement especially in a low current region.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Modelling and simulation of parallel triangular triple quantum dots (TTQD) by using SIMON 2.0

This research presents analysis of modeling on Parallel Triple Quantum Dots (TQD) by using SIMON (SIMulation Of Nano-structures). Single Electron Transistor (SET) is used as the basic concept of modeling. We design the structure of Parallel TQD by metal material with triangular geometry model, it is called by Triangular Triple Quantum Dots (TTQD). We simulate it with several scenarios using different parameters; such as different value of capacitance, various gate voltage, and different thermal condition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Interaction between ions in hot dense plasma via screened Cornell potential

Hot dense plasma with non-ideal ions and weakly coupled electrons is studied analytically in the framework of the random phase approximation. It is shown that at some plasma parameters ions interact by a screened Cornell potential. The reduction in the transport coefficients due to the localization of the electron around the ion is predicted. This prediction is confirmed by the molecular dynamics simulation of the one-component ion plasma interacting via the obtained screened Cornell type potential.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Elliptic flow due to charged hadrons for Au+Au collisions at RHIC energy 62.4 GeV

Elliptic flow is an important observable in search of Quark Gluon Plasma. The elliptic flow parameter dependence on centrality due to charged hadrons were studied using events generated by event generator AMPT at center of mass energy of 62.4 GeV per nucleon pair for Au+Au collisions. This study performed for pseudorapidity range from −0.35 to 0.35 and transverse momentum bins p{sub t} = 0.2 to 1 GeV/c and 1 to 2 GeV/c. We compared the results obtained from simulated data and RHIC-PHENIX data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Chaos control of the micro-electro-mechanical resonator by using adaptive dynamic surface technology with extended state observer

This paper addresses chaos control of the micro-electro- mechanical resonator by using adaptive dynamic surface technology with extended state observer. To reveal the mechanism of the micro- electro-mechanical resonator, the phase diagrams and corresponding time histories are given to research the nonlinear dynamics and chaotic behavior, and Homoclinic and heteroclinic chaos which relate closely with the appearance of chaos are presented based on the potential function. To eliminate the effect of chaos, an adaptive dynamic surface control scheme with extended state observer is designed to convert random motion into regular motion without precise system model parameters and measured variables. Putting tracking differentiator into chaos controller solves the ‘explosion of complexity’ of backstepping and poor precision of the first-order filters. Meanwhile, to obtain high performance, a neural network with adaptive law is employed to approximate unknown nonlinear function in the process of controller design. The boundedness of all the signals of the closed-loop system is proved in theoretical analysis. Finally, numerical simulations are executed and extensive results illustrate effectiveness and robustness of the proposed scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum-mechanical calculations of residual current density excited during gas ionisation by an intense two-colour laser pulse

By solving analytically and numerically the three-dimensional time-dependent Schrödinger equation, we have studied the excitation of a residual current density during gas ionisation by a two-colour laser pulse containing a field at the fundamental frequency and an additional field at the doubled frequency. We have found the dependences of the residual current density on the phase shift between the components of the field and on the intensity of the fundamental harmonic. It is shown that the strong-field approximation taking into account the interaction of freed electrons with the parent ion yields a good quantitative agreement with the results of direct numerical simulation. (extreme laser radiation: physics and fundamental applications)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

REIONIZATION ON LARGE SCALES. I. A PARAMETRIC MODEL CONSTRUCTED FROM RADIATION-HYDRODYNAMIC SIMULATIONS

We present a new method for modeling inhomogeneous cosmic reionization on large scales. Utilizing high-resolution radiation-hydrodynamic simulations with 2048{sup 3} dark matter particles, 2048{sup 3} gas cells, and 17 billion adaptive rays in a L = 100 Mpc h {sup –1} box, we show that the density and reionization redshift fields are highly correlated on large scales (∼> 1 Mpc h {sup –1}). This correlation can be statistically represented by a scale-dependent linear bias. We construct a parametric function for the bias, which is then used to filter any large-scale density field to derive the corresponding spatially varying reionization redshift field. The parametric model has three free parameters that can be reduced to one free parameter when we fit the two bias parameters to simulation results. We can differentiate degenerate combinations of the bias parameters by combining results for the global ionization histories and correlation length between ionized regions. Unlike previous semi-analytic models, the evolution of the reionization redshift field in our model is directly compared cell by cell against simulations and performs well in all tests. Our model maps the high-resolution, intermediate-volume radiation-hydrodynamic simulations onto lower-resolution, larger-volume N-body simulations (∼> 2 Gpc h {sup –1}) in order to make mock observations and theoretical predictions.

79 ASTRONOMY AND ASTROPHYSICS↗

Convection causes enhanced magnetic turbulence in accretion disks in outburst

We present the results of local, vertically stratified, radiation magnetohydrodynamic (MHD) shearing box simulations of magneto-rotational instability (MRI) turbulence appropriate for the hydrogen ionizing regime of dwarf nova and soft X-ray transient outbursts. We incorporate the frequency-integrated opacities and equation of state for this regime, but neglect non-ideal MHD effects and surface irradiation, and do not impose net vertical magnetic flux. We find two stable thermal equilibrium tracks in the effective temperature versus surface mass density plane, in qualitative agreement with the S-curve picture of the standard disk instability model. We find that the large opacity at temperatures near 10{sup 4} K, a corollary of the hydrogen ionization transition, triggers strong, intermittent thermal convection on the upper stable branch. This convection strengthens the magnetic turbulent dynamo and greatly enhances the time-averaged value of the stress to thermal pressure ratio α, possibly by generating vertical magnetic field that may seed the axisymmetric MRI, and by increasing cooling so that the pressure does not rise in proportion to the turbulent dissipation. These enhanced stress to pressure ratios may alleviate the order of magnitude discrepancy between the α-values observationally inferred in the outburst state and those that have been measured from previous local numerical simulations of magnetorotational turbulence that lack net vertical magnetic flux.

79 ASTRONOMY AND ASTROPHYSICS↗

Study of guided wave transmission through complex junction in sodium cooled reactor

Ultrasonic guided wave techniques are seen as suitable candidates for the inspection of welded structures within sodium cooled fast reactors (SFR), as the long range propagation of guided waves without amplitude attenuation can overcome the accessibility problem due to the liquid sodium. In the context of the development of the Advanced Sodium Test Reactor for Industrial Demonstration (ASTRID), the French Atomic Commission (CEA) investigates non-destructive testing techniques based on guided wave propagation. In this work, guided wave NDT methods are applied to control the integrity of welds located in a junction-type structure welded to the main vessel. The method presented in this paper is based on the analysis of scattering matrices peculiar to each expected defect, and takes advantage of the multi-modal and dispersive characteristics of guided wave generation. In a simulation study, an algorithm developed using the CIVA software is presented. It permits selecting appropriate incident modes to optimize detection and identification of expected flawed configurations. In the second part of this paper, experimental results corresponding to a first validation step of the simulation results are presented. The goal of the experiments is to estimate the effectiveness of the incident mode selection in plates. The results show good agreement between experience and simulation. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

SU-E-T-638: Proton Beam Delivery to a Moving Lung Tumor and Monte Carlo Simulation with TOPAS

Purpose: To estimate the dose delivered to a moving lung tumor by proton therapy beams of different modulation types, and compare with Monte Carlo predictions. Methods: A radiology support devices (RSD) phantom was irradiated with therapeutic proton radiation beams using two different types of modulation: uniform scanning (US) and double scattered (DS). The Eclipse© dose plan was designed to deliver 1.00Gy to the isocenter of a static ∼3×3×3cm (27cc) tumor in the phantom with 100% coverage. The peak to peak amplitude of tumor motion varied from 0.0 to 2.5cm. The radiation dose was measured with an ion-chamber (CC-13) located within the tumor. The time required to deliver the radiation dose varied from an average of 65s for the DS beams to an average of 95s for the US beams. Results: The amount of radiation dose varied from 100% (both US and DS) to the static tumor down to approximately 92% for the moving tumor. The ratio of US dose to DS dose ranged from approximately 1.01 for the static tumor, down to 0.99 for the 2.5cm moving tumor. A Monte Carlo simulation using TOPAS included a lung tumor with 4.0cm of peak to peak motion. In this simulation, the dose received by the tumor varied by ∼40% as the period of this motion varied from 1s to 4s. Conclusion: The radiation dose deposited to a moving tumor was less than for a static tumor, as expected. At large (2.5cm) amplitudes, the DS proton beams gave a dose closer to the desired dose than the US beams, but equal within experimental uncertainty. TOPAS Monte Carlo simulation can give insight into the moving tumor — dose relationship. This work was supported in part by the Philips corporation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Influence of grain charge gradients on the dynamics of macroparticles in an electrostatic trap

An analytical model of anomalous heating of charged dust grains (macroparticles) caused by their stochastic motion in a bounded plasma volume is proposed. Analytical expressions allowing one to describe the pumping (heating) of interacting grains with additional stochastic energy due to grain charge gradients are derived. The analytical results are verified by numerical simulation of the problem. It is shown that spatial variations in the charges of dust grains can lead to their anomalous heating in laboratory plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the effect of ballistic overflow on the temperature dependence of the quantum efficiency of InGaN/GaN multiple quantum well light-emitting diodes

The dependences of the quantum efficiency of InGaN/GaN multiple quantum well light-emitting diodes on the temperature and excitation level are studied. The experiment is performed for two luminescence excitation modes. A comparison of the results obtained during photo- and electroluminescence shows an additional (to the loss associated with Auger recombination) low-temperature loss in the high-density current region. This causes inversion of the temperature dependence of the quantum efficiency at temperatures lower than 220–300 K. Analysis shows that the loss is associated with electron leakage from the light-emitting-diode active region. The experimental data are explained using the ballistic-overflow model. The simulation results are in qualitative agreement with the experimental dependences of the quantum efficiency on temperature and current density.

36 MATERIALS SCIENCE↗

The Virtual Test Bed (VTB) repository: a library of multiphysics reference reactor models using NEAMS tools

With the next generation of nuclear reactors under development, modeling and simulation (MS) tools are being developed by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program in order to support their design, licensing, and future operation. Mirroring the physical test beds currently under construction (i.e., EBR-II and ZPPR), the Virtual Test Bed (VTB) was launched by the National Reactor Innovation Center (NRIC) in collaboration with NEAMS to support the advanced reactor community. This collaborative effort, which involves multiple teams at both Idaho National Laboratory and Argonne National Laboratory aims to use NEAMS tools to model a wide range of reactor designs. Those models are automatically tested to ensure their continued functionality as the tools are further developed. Examples are extensively documented, each acting as a tutorial for applying the relevant NEAMS tools to that reactor design. Currently, five advanced reactor types (with a total of eight specific design variants) are simulated by a variety of different models. These models range from steady-state, core multiphysics simulations to integrated plant analysis during loss-of flow transients. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Thermal and Chemical Evolution of Collapsing Filaments

Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z ≈ 0.1Z ⊙ filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10 -3 Z ⊙ filaments, the collapse proceeds much more slowly. This is due mostly to the lower initial temperatures, which leads to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbusting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occur. We find that we achieve similar accretion rates as NGC 5253, but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

79 ASTRONOMY AND ASTROPHYSICS↗